Cis Modes Research Articles

Fused N-Heterocyclic-Bridged Isomeric Diruthenium Complexes [(acac)2Ru(μ-DIPQD)Ru(acac)2]n, n = +2, + 1, 0, -1, -2.

π-Conjugated bridged isomeric diruthenium(II) complexes [(acac)2RuII(μ-DIPQD)RuII(acac)2], 1 (trans) and 2 (cis) (acac- = acetylacetonate, (8E,16E)-N8,N16-diphenylindeno[1,2-b]indeno[2',1':5,6]pyrazino[2,3-g]quinoxaline-8,16-diimine (trans-DIPQD), and (12E,16E)-N12,N16-diphenylindeno[1,2-b]indeno[1',2':5,6]pyrazino[2,3-g]quinoxaline-12,16-diimine (cis-DIPQD) were separated and structurally characterized. The structures of the rac (ΔΔ/ΛΛ) forms of 1 and 2 exhibit two units of {Ru(acac)2}, linked to adjacent pyrazine and imine nitrogen donors of the bridge (DIPQD) in trans and cis modes, with metal-metal separations of 9.050 and 6.330 Å, respectively. The packing diagrams of 1 and 2 revealed an intermolecular π···π stacking interaction (3.202-3.398 Å) involving the face-to-face arrangement of the aromatic rings of DIPQD in adjacent molecules and varying solid-state packing modes, slipped stacking in the former versus brick-layer stacking in the latter. The electronic forms associated with multiple reversible one-electron redox steps of 1 and 2 were addressed by DFT (MO composition, Mulliken spin density distribution), supported by EPR of intermediate paramagnetic states and by UV-vis-NIR spectroelectrochemistry in all redox states. The results reveal similar electronic forms along the redox series irrespective of their isomeric identities in 1 and 2, viz., primarily metal-based oxidations ([(acac)2RuII(μ-DIPQD)RuIII(acac)2]+, 1+/2+, S = 1/2; [(acac)2RuIII(μ-DIPQD)RuIII(acac)2]2+, 12+/22+, S = 1) and bridge-based reductions ([(acac)2RuII(μ-DIPQD•-)RuII(acac)2]-, 1•-/2•-, S = 1/2; [(acac)2RuII(μ-DIPQD2-)RuII(acac)2]2-, 12-/22-, S = 1). TD-DFT analysis of the electronic transitions in the complexes suggests bridge-targeted mixed metal/ligand-based multiple charge transfer transitions over the visible to NIR region in all redox states, while a weak band involving the radical bridge appeared in the long-wavelength region (∼2000 nm) in 1•-/2•-.

XL-Xantphos: Design and Synthesis of a Mechanistic Probe of Xantphos O-Coordination in Catalytic Reactions

The synthesis and characterization of an analog of the Xantphos ligand that is geometrically incapable of coordination of the xanthene bridging oxygen atom is reported. This new ligand, XL-Xantphos, ((9,9-dimethyl-9H-xanthene-4,5-diyl)bis(4,1-phenylene))bis(diphenylphosphane), was studied in homogeneous, catalytic reactions for comparison with Xantphos. The XL-Xantphos ligand performed essentially identically to Xantphos in Rh-catalyzed hydroformylation of 1-octene, which suggests that the high regioselectivity for linear aldehyde is due to the large bite angle of these ligands and is not influenced by oxygen coordination to the metal. The Pd-catalyzed amidocarbonylation of 4-bromoanisole with dimethylhydroxylamine hydrochloride similarly showed no difference between Xantphos and XL-Xantphos. Computations on Pd(II) phosphine complexes at the DLPNO–CCSD(T) level of theory indicated that these ligands have different preferences for cis and trans coordination modes. The XL-Xantphos ligand has a thermodynamic...

New mixed amino acids complexes of iron(III) and zinc(II) with isonitrosoacetophenone: Synthesis, spectral characterization, DFT study and anticancer activity

New mixed Fe(III) and Zn(II) complexes with isonitrosoacetophenone (HINAP) and l-amino acids (such as l-histidine, l-phenylalanine and l-proline) have been synthesized and characterized by elemental analyses, UV-Vis, IR and ESR spectroscopy and thermal analyses. The values of molar conductance of the complexes in DMSO solution at 10-3 M concentration indicate their non-electrolyte nature. IR spectroscopy has revealed the coordination of deprotonated ligands to metal through nitrogen and oxygen atoms in an N2O2 arrangement. Density functional theory (DFT) calculations were performed using the hybrid functional of Truhlar and Zhao (M06) with basis set of double zeta quality LANL2DZ to evaluate the cis and trans coordination modes and to ascertain dipole moment, HOMO-LUMO energy gap, chemical hardness, softness and electrophilicity. The magnetic moments and ESR measurements suggest that there is an admixture of S = 5/2 and S = 1/2 spins in Fe(III) complexes. UV-Visible spectra indicate a distorted octahedral geometry around the metal ions. Thermal analyses show the presence of hydrated and coordinated water. The antimicrobial activity was investigated against (G+ and G-) bacteria (Staphylococcus aureus, bacillus subtilis, Escherichia coli, Pseudomonas aeruginosa) and fungi (Candida albicans). The iron and zinc complexes were found to be more active against Gram-positive than Gram negative bacteria. They also show considerable growth inhibition against the fungi tested. In vitro antitumor activity assayed against cancer cell lines of the HEP2 type (cancer cells of the larynx) exhibited significant toxicity of the ligands and their mixed complexes.

LncGata6-controlled stemness in regeneration and cancer.

Long-noncodingRNAs (lncRNAs) have been proposed as a critical regulator of various cellularprocesses including cell fate decision and cell proliferation (1,2).Mechanistically, lncRNAs control various gene expressions by recruiting thechromatin modifiers in cis and trans modes (1). Transcription oflncRNAs itself also can activate or suppress the neighboring gene expression bythe transcriptional interference through regulatory sequences (1,3). lncRNAsare also involved in a wide range of protein and RNA regulatory functions, suchas scaffoldings of proteins and RNAs, protein and RNA decoys, and functionalmicro-peptides production (1). Aberrant regulation of lncRNA-mediated cellularprocesses is implicated in human disease including cancer (4,5). The recenttechnologic advance including the single-cell RNA sequencing (scRNA-seq), andgene editing, genetically engineered mouse (GEM) models has made it feasible toelucidate the various roles of lncRNAs in the normal tissue physiology and thepathologic conditions including tumorigenesis and metastasis (2,6).

Structural Basis for Interactions Between Contactin Family Members and Protein-tyrosine Phosphatase Receptor Type G in Neural Tissues

Protein-tyrosine phosphatase receptor type G (RPTPγ/PTPRG) interacts in vitro with contactin-3-6 (CNTN3-6), a group of glycophosphatidylinositol-anchored cell adhesion molecules involved in the wiring of the nervous system. In addition to PTPRG, CNTNs associate with multiple transmembrane proteins and signal inside the cell via cis-binding partners to alleviate the absence of an intracellular region. Here, we use comprehensive biochemical and structural analyses to demonstrate that PTPRG·CNTN3-6 complexes share similar binding affinities and a conserved arrangement. Furthermore, as a first step to identifying PTPRG·CNTN complexes in vivo, we found that PTPRG and CNTN3 associate in the outer segments of mouse rod photoreceptor cells. In particular, PTPRG and CNTN3 form cis-complexes at the surface of photoreceptors yet interact in trans when expressed on the surfaces of apposing cells. Further structural analyses suggest that all CNTN ectodomains adopt a bent conformation and might lie parallel to the cell surface to accommodate these cis and trans binding modes. Taken together, these studies identify a PTPRG·CNTN complex in vivo and provide novel insights into PTPRG- and CNTN-mediated signaling.

Validation of Cis and Trans Modes in Multistep Phosphotransfer Signaling of Bacterial Tripartite Sensor Kinases by Using Phos-Tag SDS-PAGE.

Tripartite sensor kinases (TSKs) have three phosphorylation sites on His, Asp, and His residues, which are conserved in a histidine kinase (HK) domain, a receiver domain, and a histidine-containing phosphotransmitter (HPt) domain, respectively. By means of a three-step phosphorelay, TSKs convey a phosphoryl group from the γ-phosphate group of ATP to the first His residue in the HK domain, then to the Asp residue in the receiver domain, and finally to the second His residue in the HPt domain. Although TSKs generally form homodimers, it was unknown whether the mode of phosphorylation in each step was intramolecular (cis) or intermolecular (trans). To examine this mode, we performed in vitro complementation analyses using Ala-substituted mutants of the ATP-binding region and three phosphorylation sites of recombinant ArcB, EvgS, and BarA TSKs derived from Escherichia coli. Phosphorylation profiles of these kinases, determined by using Phos-tag SDS-PAGE, showed that the sequential modes of the three-step phosphoryl-transfer reactions of ArcB, EvgS, and BarA are all different: cis-trans-trans, cis-cis-cis, and trans-trans-trans, respectively. The inclusion of a trans mode is consistent with the need to form a homodimer; the fact that all the steps for EvgS have cis modes is particularly interesting. Phos-tag SDS-PAGE therefore provides a simple method for identifying the unique and specific phosphotransfer mode for a given kinase, without taking complicated intracellular elements into consideration.

Synthesis, characterization, electrochemical studies and DFT calculations of amino acids ternary complexes of copper (II) with isonitrosoacetophenone. Biological activities

Three mixed complexes having formula [Cu(INAP)L(H2O)2] where INAP=deprotonated isonitrosoacetophenone and L=deprotonated amino acid such as histidine, phenylalanine and tryptophan have been synthesized. They have also been characterized using elemental analyses, molar conductance, UV–Vis, IR and ESR spectra. The value of molar conductance indicates them to be non-electrolytes. The spectral studies support the binding of the ligands with two N and two O donor sites to the copper (II) ion, giving an arrangement of N2O2 donor groups. Density Functional Theory (DFT) calculations were applied to evaluate the cis and trans coordination modes of the two water molecules. The trans form was shown to be energetically more stable than the cis one.The ESR data indicate that the covalent character of the metal–ligand bonding in the copper (II) complexes increases on going from histidine to phenylalanine to tryptophan.The electrochemical behavior of the copper (II) complexes was determined by cyclic voltammetry which shows that the chelate structure and electron donating effects of the ligands substituent are among the factors influencing the redox potentials of the complexes.The antimicrobial activities of the complexes were evaluated against several pathogenic microorganisms to assess their antimicrobial potentials. The copper complexes were found to be more active against Gram-positive than Gram-negative bacteria.Furthermore, the antioxidant efficiencies of the metal complexes were determined by 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity. The antioxidant activity of the complexes indicates their moderate scavenging activity against the radical DPPH.

A new platinum complex with tryptophan: Synthesis, structural characterization, DFT studies and biological assays in vitro over human tumorigenic cells

A new platinum(II) complex with the amino acid L-tryptophan (trp), named Pt-trp, was synthesized and characterized. Elemental, thermogravimetric and ESI-QTOF mass spectrometric analyses led to the composition [Pt(C11H11N2O2)2]⋅6H2O. Infrared spectroscopic data indicate the coordination of trp to Pt(II) through the oxygen of the carboxylate group and also through the nitrogen atom of the amino group. The 13C CP/MAS NMR spectroscopic data confirm coordination through the oxygen atom of the carboxylate group, while the 15N CP/MAS NMR data confirm coordination of the nitrogen of the NH2 group to the metal. Density functional theory (DFT) studies were applied to evaluate the cis and trans coordination modes of trp to platinum(II). The trans isomer was shown to be energetically more stable than the cis one. The Pt-trp complex was evaluated as a cytotoxic agent against SK-Mel 103 (human melanoma) and Panc-1 (human pancreatic carcinoma) cell lines. The complex was shown to be cytotoxic over the considered cells.

Ephrin-Mediated cis-Attenuation of Eph Receptor Signaling Is Essential for Spinal Motor Axon Guidance

Axon guidance receptors guide neuronal growth cones by binding in trans to axon guidance ligands in the developing nervous system. Some ligands are coexpressed in cis with their receptors, raising the question of the relative contribution of cis and trans interactions to axon guidance. Spinal motor axons use Eph receptors to select a limb trajectory in response to trans ephrins, while expressing ephrins in cis. We show that changes in motor neuron ephrin expression result in trajectory selection defects mirrored by changes in growth cone sensitivity to ephrins in vitro, arguing for ephrin cis-attenuation of Eph function. Furthermore, the relative contribution of trans-signaling and cis-attenuation is influenced by the subcellular distribution of ephrins to membrane patches containing Eph receptors. Thus, growth cone ephrins are essential for axon guidance in vivo and the balance between cis and trans modes of axon guidance ligand-receptor interaction contributes to the diversity of axon guidance signaling responses.

Anion Photoelectron Spectroscopy of C3N− and C5N−

Anion photoelectron spectroscopy of C(3)N(-) and C(5)N(-) is performed using slow electron velocity-map imaging (SEVI) and field-free time-of-flight (TOF), respectively. The SEVI spectrum exhibits well-resolved vibrational transitions from the linear C(3)N(-) ground state to the corresponding C(3)N ground state. The TOF spectrum comprises transitions arising from the linear C(5)N(-) ground state to the corresponding neutral ground and excited states. This study yields the adiabatic electron affinities of C(3)N and C(5)N to be 4.305 +/- 0.001 and 4.45 +/- 0.03 eV, respectively, and a term value of 560 +/- 120 cm(-1) for the A(2)Pi state of C(5)N. Vibrational frequencies for the degenerate cis and trans bending modes of C(3)N(-) are also extracted.

1D chain Cd(II) and Co(II) coordination polymers: Synthesis, crystal structures and luminescence properties

Two novel 1D infinite chain coordination polymers, [CdL(NO 3) 2] n and [CoL(NO 3) 2] n (L = 4,4′-bis[2-(2-pyridyl)ethenyl]biphenyl) have been prepared by reacting Cd(NO 3) 2 and Co(NO 3) 2 with the novel ligand L. Complexes 1 and 2 have been characterized by elemental analysis, IR and single crystal X-ray diffraction determination. The metal ions in the polymers have six coordinate pseudo octahedral structures with two pyridyl nitrogen atoms of L and four oxygen atoms of nitrate. The ligand coordinates to metal ions forming bridges in different geometries ( cis and trans coordination modes). The results of TGA determination show that the coordination polymers are quite thermally stable. The complexes exhibit a strong emission band with the maximum intensity at 524 and 545 nm in solid-state, respectively, upon excitation at 350−450 nm.

Self-Assembly of cis and trans Forms of the Copper(II) Complex with 1-Aminocyclopropane-1-carboxylate into Discrete Trimers in the Solid State

A copper(II) complex with 1-aminocyclopropane-1-carboxylic acid assembles by apical Cu...O bonds and hydrogen-bonding interactions into discrete trimeric units that exhibit both cis and trans binding modes.

Magnetic circular dichroism study of Fe∕Co∕Cu(001) using electron yield x-ray absorption spectroscopy with different probe depths

To obtain depth-resolved magnetic information from Fe films grown on fcc Co∕Cu(001), we have used various signal sources for the detection of x-ray absorption spectroscopy. These include total electron yield (TEY) and partial electron yield (PEY) of inelastic electrons at various kinetic energies between 70 and 470eV as well as PEY using photoelectrons at a fixed binding energy (constant initial state: CIS) near the Fermi level. Inelastic electron yield at electron emission angles up to 87° from the surface normal was found to be as nonsurface sensitive as TEY, however, the CIS mode shows a shorter information depth, comparable to the inelastic mean free path of photoelectrons. No difference in the dichroic signal at the Fe L3 edge was found between the CIS and TEY modes for a 2-monolayer (ML) Fe∕Co film, but an 8-ML Fe∕Co film showed a much higher dichroic signal in the CIS mode than that in the TEY mode. This is consistent with a homogeneous magnetic film at an Fe thickness of 2 ML and a nonhomogeneous magnetic film with a live ferromagnetic layer on the surface with nonferromagnetic underlayers at an Fe thickness of 8 ML. Thus, it is possible to extract depth-resolved magnetic information from x-ray magnetic circular dichroism by combining the surface sensitive CIS mode with other detection modes with less surface sensitivity.

Structural influence of cis and trans coordination modes of multi-modal ligands upon coordination polymer dimensionality

Control over ligand donor arrangement leads to structural discrimination between one- and two-dimensions in two coordination frameworks, {[AgNO3]2L}∞, formed between AgNO3 and hexadentate multi-modal ligands.

The High-Resolution Fourier Transform Infrared Spectrum of Isocyanogen, CNCN: Rovibrational Analysis of the ν4, ν5, and ν4 + ν5 Band Systems and the Fermi Dyad ν3 and 2ν4

The high-resolution gas-phase Fourier transform infrared spectrum of the linear molecule isocyanogen, CNCN, has been measured between 150 and 1300 cm−1 with an unapodized resolution of 0.0018 cm−1. The band systems due to the excitation of the cis and trans bending modes ν5 and ν4 around 194.8 and 463.5 cm−1, respectively, have been analyzed. Additionally the combination band system ν5 and ν4 around 659.0 cm−1 and the transitions to the Fermi resonance pair ν3 and 2ν4 around 875 and 975 cm−1, respectively, were analyzed. Furthermore, two components of the related Fermi triad could be assigned. Constants of a power series in J(J + 1) for the numerous subbands as well as constants of an effective Hamiltonian (K. M. T. Yamada, F. W. Birss, and M. R. Aliev, J. Mol. Spectrosc.112, 347-356, 1985) are presented.

Selective UV Resonance Raman Excitation of Vinyl Group Vibrations in an Isomer of Crotyl Chloride

The Raman spectra of cis, trans, and vinyl isomers of crotyl chloride (i.e., cis and trans 1-chloro-2-butene, and 3-chloro-1-butene) have been excited at 218 nm and at 231 nm. With 218-nm excitation the ethylenic mode belonging to the vinyl isomer is only modestly preresonance enhanced. On the other hand, the preresonance enhancement of the peaks belonging to the cis and trans isomers is very noticeable and nearly identical in energy to the peaks of cis and trans polybutadiene, which occur at 1655 and 1665 cm−1, respectively. However, with 231-nm excitation the vinyl-isomer ethylenic mode at 1633 cm−1 is very strongly enhanced, while the cis and trans isomer modes show no corresponding enhancement, but appear to decrease in relative intensity. Responsibility for the strong vinyl group enhancement is assigned to an electronic transition observed as a broad shoulder near 230 nm. By exciting at 231 nm it is possible to detect small amounts of the vinyl isomer in the presence of cis and trans crotyl chloride. Remarkably strong enhancement under 231-nm excitation has been noted as well for the first overtone of the vinyl ethylenic mode observed at 3263 cm−1.

Observation of bending modes in the X2 π u state of the acetylene ion using He(I) photoelectron spectrometry

Excitations of bending modes in transitions from a linear ground state to a linear ionic state are normally very weak in He (I) photoelectron spectra; however, we have recently shown that, using a high resolution, high sensitivity photoelectron spectrometer, it is possible to observe these weak bending modes and that the occurrence of such transitions is not uncommon. With this in mind, we have re-examined the spectrum of acetylene and have observed several new features attributable to the cis and/or trans bending modes in the X2πu ground state of the ion.

Core threshold photoemission spectroscopy from the As 3d core level of GaAs (110) and effects of Ge chemisorption

We have investigated the excitation of the As 3d core level of clean and Ge covered GaAs (110) surfaces into low lying conduction band states by observing core-hole decay emission. The investigation was carried out by using synchrotron radiation to record photoemission spectra in the CIS and EDC modes. In contrast to the Ga 3d core excitation, the As 3d core excitation was found to be nonexcitonic in character. The CIS shows three structures at hυ = 43.0, 46.1, and 49.5 eV, which were strongly influenced by Ge-chemisorption. With about a monolayer of Ge, the structures are reduced to a considerably larger degree than the photoemission structure associated with the Ga 3d exciton. The As 3d core level is excited into surface related p-like states lying 2.6, 5.7, and 9.1 eV above the valence band maximum, ’’followed’’ by the radiationless Auger decay of the core holes. The inferred conduction band states are compared to recent band calculations and the state at 2.6 eV is assigned to the Ga-dangling-bond surface state. With the assumption that the As 3d core excitation is to the same surface state as the Ga 3d core excitation, we estimate the exciton binding energy for the latter excitations to be ∠1.8 eV.