Ring Interactions Research Articles

Structural view of the yeast Dam1 complex, a ring-shaped molecular coupler for the dynamic microtubule end.

In a dividing eukaryotic cell, proper chromosome segregation requires the dynamic yet persistent attachment of kinetochores to spindle microtubules. In the budding yeast Saccharomyces cerevisiae, this function is especially crucial because each kinetochore is attached to a single microtubule; consequently, loss of attachment could lead to unrecoverable chromosome loss. The highly specialized heterodecameric Dam1 protein complex achieves this coupling by assembling into a microtubule-encircling ring that glides near the end of the dynamic microtubule to mediate chromosome motion. In recent years, we have learned a great deal about the structural properties of the Dam1 heterodecamer, its mechanism of self-assembly into rings, and its tethering to the kinetochore by the elongated Ndc80 complex. The most remarkable progress has resulted from defining the fine structures of helical bundles within Dam1 heterodecamer. In this review, we critically analyze structural observations collected by diverse approaches with the goal of obtaining a unified view of Dam1 ring architecture. A considerable consistency between different studies supports a coherent model of the circular core of the Dam1 ring. However, there are persistent uncertainties about the composition of ring protrusions and flexible extensions, as well as their roles in mediating ring core assembly and interactions with the Ndc80 complex and microtubule.

Synthesis, crystal structure, hirshfeld surface analysis, DFT computations and molecular dynamics study of 2-(benzyloxy)-3-phenylquinoxaline

Quinoxalines are regarded as a promising class of biologically active agents, and they constitute useful intermediates in organic synthesis. In this study, we report synthesis, single crystal X-ray diffraction, and computational investigations of the 2-(benzyloxy)-3-phenylquinoxaline (O-alkylated isomer). Single crystal X-ray diffraction investigations revealed that the quinoxaline unit is not entirely planar. In the crystal form, inversion-related molecules form dimers through slipped π-stacking interactions between quinoxaline units. These are coupled together into chains extending along the c-axis direction by C–H···π(ring) interactions. Inspection of the Hirshfeld surface analysis revealed that H⋯H (48.8%), C⋯H/H⋯C (35.1%) and H⋯N/N⋯H (7.3%) are the main interactions that govern the crystal packing of the presented structure. The optimized geometry, Natural Bond Orbital (NBO), Fukui functions and all other structural and electronic features were calculated by using Density Functional Theory (DFT) at B3LYP employing 6–311++G(d,p) basis set. The HOMO and LUMO distribution showed a pronounced electronic density over the quinoxaline moiety. Computed NBO analysis explored the interactions as well as charge transfers among different orbitals and lone pairs occurring within the compound. Radial distribution functions (RDF) were calculated using molecular dynamics (MD) simulations to study interactions of water molecules with atoms of the title compound.

Keep the Phone in Your Pocket

Previous studies have shown that visually impaired users face a unique set of pain points in smartphone interaction including locating and removing the phone from a pocket, two-handed interaction while holding a cane, and keeping personal data private in a public setting. In this paper, we present a ring-based input interaction that enables in-pocket smartphone operation. By wearing a ring with an Inertial Measurement Unit on the index finger, users can perform gestures on any surface (e.g., tables, thighs) using subtle, one-handed gestures and receive auditory feedback via earphones. We conducted participatory studies to obtain a set of versatile commands and corresponding gestures. We subsequently trained an SVM model to recognize these gestures and achieved a mean accuracy of 95.5% on 15 classifications. Evaluation results showed that our ring interaction is more efficient than some baseline phone interactions and is easy, private, and fun to use.

THE EFFECT OF THE RADIAL CLEARANCES ON THE DYNAMIC PROCESSES IN ROLLING BEARINGS

A method for calculating the parameters of shock pulses generated in rolling bearings due to the presence of radial clearance in them is proposed. The method is a further development of theoretical research in the scientific direction of vibration-pulse diagnostics in relation to the operational assessment of the technical condition of bearing units as components of the gear drive mechanism, which largely determine the drive resource as a whole. The calculation is based on the consideration of the precession movement of the bearing axis, which it makes during the rotation of its shaft, and the theory of shock interaction of elastic bodies by G. Hertz. The mechanism of occurrence of shock pulses has been studied with an additional introduction to the calculation of the radial force acting on the shaft. It is shown that wear, which causes an increase in the working radial clearance between the races and the rolling bodies in the bearing, increases the speed and amplitude of the impact interaction of the inner ring with the rolling bodies. An example of calculating the parameters of shock pulses in ball radial single-row bearings of the 307 series is given. Conclusions are made about the prospects of using the developed method for diagnostics and forecasting the remaining life of bearings of transmission units of mobile machines.

Preparation and Structural Characterization of Bis (N, N’-phenanthroline)- bis (O, O’-nitrate) Cd (II) Complex

An eight-coordinated Cd (II) complex, bis (N,N’-phenanthroline)-bis (O,O’-nitrate) Cd (II) (1), was synthesized using 1, 10-phenanthroline and cadmium nitrate tetrahydrate as raw materials. The structural analyses of Cd(II) complex 1 shows that the compound 1 belongs to monoclinic, space group C12/c1 (no.15) with a = 11.4490(5) Å, b = 15.3716 (6) Å, c = 13.2153 (6) Å, β = 102.892 (5)º, V=2267.13 (17) Å3, Z = 4, Dc = 1.749 mg·m−3, μ = 1.020 mm−1, F(000) = 1192, and final R1 = 0.0392, ωR2 = 0.0827. The Cd (II) complex 1 forms 1D chained structure by the π-π interaction of phenanthroline rings..

Crystal structure, Hirshfeld surface analysis, inter-action energy and DFT studies of 4-[(4-allyl-2-meth-oxy-phen-oxy)meth-yl]-1-(4-meth-oxy-phen-yl)-1H-1,2,3-triazole.

In the title mol-ecule, C20H21N3O3, the allyl substituent is rotated out of the plane of its attached phenyl ring [torsion angle 100.66 (15)°]. In the crystal, C-HMthphn⋯OMthphn (Mthphn = meth-oxy-phen-yl) hydrogen bonds lead to the formation of (100) layers that are connected into a three-dimensional network by C-H⋯π(ring) inter-actions, together with π-π stacking inter-actions [centroid-to-centroid distance = 3.7318 (10) Å] between parallel phenyl rings. Hirshfeld surface analysis indicates that the most important contributions to the crystal packing are from H⋯H (48.7%) and H⋯C/C⋯H (23.3%) inter-actions. Computational chemistry reveals that the C-HMthphn⋯OMthphn hydrogen bond energy is 47.1 kJ mol-1. The theoretical structure, optimized by density functional theory (DFT) at the B3LYP/ 6-311 G(d,p) level, is compared with the experimentally determined mol-ecular structure. The HOMO-LUMO behaviour was elucidated to determine the energy gap.

Crystal structures of 6-cyclo-propyl-1,3-diphenylfulvene and 6-(2,3-di-meth-oxy-naphth-yl)-1,3-di-phenylfulvene.

The title compounds, 6-cyclo-propyl-1,3-diphenylfulvene, C21H18, [systematic name: 5-(cyclo-propyl-methyl-idene)-1,3-di-phen-yl-cyclo-penta-1,3-diene], 1, and 6-(2,3-di-meth-oxy-naphth-yl)-1,3-diphenylfulvene, C30H24O2, {systematic name: 5-[(3,4-di-meth-oxy-naphthalen-2-yl)methyl-idene]-1,3-di-phenyl-cyclo-penta-1,3-di-ene}, 2, were prepared from 1,3-di-phenyl-cyclo-penta-diene, pyrrolidine, and the corresponding aldehydes in an ethano-lic solution. Each structure crystallizes with one mol-ecule per asymmetric unit and exhibits the alternating short and long bond lengths typical of fulvenes. A network of C-H⋯C ring inter-actions as well as C-H⋯O inter-actions is observed, resulting in the compact packing found in each structure.

Metal–ring interactions in actinide sandwich compounds: A combined normalized elimination of the small component and local vibrational mode study

The relativistic Hamiltonian Normalised Elimination of the Small Component with atomic unitary transformation (NESCau) was used for the first time to calculate geometries and harmonic vibrational frequencies of actinide sandwich compounds (An: Th, Pa, U, Np, Pu; ). In addition, the Local Vibrational Mode analysis, the Natural Bond Orbital analysis, and the Atoms in Molecules analysis were applied to quantitatively assess the intrinsic strength and the nature of the An-ring interactions. Our results show that actinide sandwich compounds prefer strong covalent interactions between actinide and carbon atoms, similar to those found for homologous ferrocene-type complexes . The metal centre rather than the ring size plays a key role in the strength of those interactions.

Conversion of Fluorescence Signals into Optical Fingerprints Realizing High-Throughput Discrimination of Anionic Sulfonate Surfactants with Similar Structure Based on a Statistical Strategy and Luminescent Metal-Organic Frameworks.

To date, the effective discrimination of anionic sulfonate surfactants with tiny differences in structure, considered as environmentally noxious xenobiotics, is still a challenge for traditional analytical techniques. Fortunately, a sensor array becomes the best choice for recognizing targets with similar structures or physical/chemical properties by virtue of principal component analysis (PCA, a statistical technique). Herein, because of the beneficial construction of the statistical strategy and use of two types of luminescent metal-organic frameworks (LMOFs, NH2-UiO-66 and NH2-MIL-88) as sensing elements, high-throughput discrimination and detection of five anionic sulfonate surfactants and their mixtures are nicely realized for the first time. Significantly, the stacking interaction of aromatic rings and dynamic quenching play essential roles in the generation of diverse fluorescence responses and unique fingerprint maps for individual anionic sulfonate surfactants. Moreover, the mixtures of anionic sulfonate surfactants are also satisfactorily distinguished in environmental water samples, demonstrating the practicability of the sensor array. On the basis of the PCA method, this strategy converts general fluorescence signals into unique optical fingerprints of individual analytes, providing a new opportunity for the application of LMOFs in the field of analytes recognition.

C–H···π(metal–ligand ring) interaction in a mesaconate bridged Cd(II) 1-D coordination polymer: structural elucidation, theoretical study, and photophysical properties

A Cd(II)-based one-dimensional coordination polymer (1-D CP), [Cd2(mes)2(4-phpy)4] (1), was prepared using mesaconic acid (H2mes) and 4-phenyl pyridine (4-phpy) mixed ligand system. Compound 1 has been characterized by elemental analysis, infrared spectroscopy, thermogravimetric analysis (TGA), powder X-ray diffraction (PXRD) pattern and single crystal X-ray diffraction (SCXRD) techniques. Structural elucidation reveals a 1-D chain which contains a 14-membered metal-ligand ring composed of two mes ligands and two Cd(II) centers. Further, the 1-D chains are assembled into a two-dimensional (2-D) supramolecular network by C–H···π(metal-ligand ring) interactions. The fluorescence lifetime of 1 shows a good range of average lifetime. The theoretical band gap has also been calculated by density functional theory (DFT) computations, which shows that 1 may possess semiconducting properties.

Ultrasonic-assisted synthesis and structural characterization of a novel 3D Pb(II) metal-organic CPs and their nanostructures

A new sonochemical synthesis was utilized to synthesize nanostructures of a novel lead (II) metal-organic coordination polymer, {[Pb2(2-apinh)2(Br)4]}n (1) (2-apinh: 2-acetylpyridine isonicotinoylhydrazone). The effects of reaction time, concentrations, and the irradiation power have been investigated and the optimized synthesis parameters were identified. The compound has been categorized by elemental analysis, scanning electron microscopy (SEM), FT-IR spectroscopy, thermogravimetric analysis (TGA), differential scanning calorimetry (DSC) powder X-ray diffraction (PXRD), and single-crystal X-ray analysis.The crystal form of 1 shows two different Pb coordination spheres in the structure, with the crystal taking three-dimensional coordination polymer shape. The coordination numbers of lead (II) centers are seven and eight with holodirected and hemidirected coordination sphere. The adjoining chains are linked by pi-pi interactions of the adjacent aromatic 2-apinh rings and several other relatively weak interactions. These weak interactions further enable the self-assembly of 1 to form a 3D metal-organic coordination polymer.

2,4-D adsorption from agricultural subsurface drainage by canola stalk-derived activated carbon: insight into the adsorption kinetics models under batch and column conditions

In this study, the experimental and kinetic modeling investigations were performed to evaluate the ability of mesoporous and microporous canola stalk-derived activated carbon (CSAC) on 2,4-dichlorophenoxyacetic acid (2,4-D) removal from synthetic and natural water in both batch and continuous systems. Three empirical models (pseudo-first-order equation (PFOE), pseudo-second-order equation (PSOE), and the Elovich equation (EE)) and three theoretical models (film diffusion model (FDM), particle diffusion model (PDM), and second-order chemical reaction rate model (SOCRRM)) were compared in terms of diffusion coefficients, maximum 2,4-D adsorption, and rate constants at various operating conditions. CSAC was prepared at 600°C and activated with water steam under a controlled flow and subsequently characterized by various analytical methods. The results showed that the maximum 2,4-D uptake by CSAC was achieved as 135.8mgg-1 under a pH of 2 and an initial 2,4-D concentration of 150mgL-1. The CSAC removed 38.3% of Na+, 43.49% of K+, 8.96% of Mg2+, 45.14% of Ca2+, 17.2% of Cl-1, 39.48% of HCO3-, 63.74% of SO42-, and 100% of the herbicide from agricultural subsurface drainage water and also retained its usability after regenerated by acetone for five cycles. It was concluded that the 2,4-D was adsorbed on the surface of the CSAC through its aromatic ring interaction with the reactive functional groups of the adsorbent. The model result indicated that the PDM is the best-fitting kinetic model for the adsorption of 2,4-D by CSAC, followed by FDM, SOCRRM, PSOE, PFOE, and EE. The mass balance equation based on PDM describes the dynamic behavior of the column satisfactorily. Graphical abstract.

The role of benzene rings in monitoring amino acids by SERS

Two aromatic compounds, l-phenylalanine and l-tyrosine, are used to study the role of phenyl rings in SERS. Through the interaction of benzene ring and silver sol, it is found that the signal of SERS is greatly enhanced compared with conventional Raman. The effects of sodium borohydride, anti-destructive thrombosis, formaldehyde, tannic acid, and sodium citrate as a reducing agent on silver sol was prepared by reducing AgNO3, on SERS with amino acid were studied. It was found that the silver sol prepared by reducing sodium nitrate by sodium borohydride had the best reinforcing effect.

Crystal structure, Hirshfeld surface analysis and DFT studies of 1,3-bis-[2-meth-oxy-4-(prop-2-en-1-yl)phen-oxy]propane.

The asymmetric unit of the title compound, C23H28O4, comprises two half-mol-ecules, with the other half of each mol-ecule being completed by the application of twofold rotation symmetry. The two completed mol-ecules both have a V-shaped appearance but differ in their conformations. In the crystal, each independent mol-ecule forms chains extending parallel to the b axis with its symmetry-related counterparts through C-H⋯π(ring) inter-actions. Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯H (65.4%), H⋯C/C⋯H (21.8%) and H⋯O/O⋯H (12.3%) inter-actions. Optimized structures using density functional theory (DFT) at the B3LYP/6-311 G(d,p) level are compared with the experimentally determined mol-ecular structures in the solid state. The HOMO-LUMO behaviour was elucidated to determine the energy gap.

Synthesis and Crystal Structure of A Novel Cd (II) Complex with Pyridine-2-aldehyde-4- (2-methylphenyl)-3- thiosemioarbazlde Ligand

A new Cd (II) complex, [Cd (L)2]·(NO3)2·H2O (L = pyridine-2-aldehyde-4-(2-methylphenyl)-3-thiosemioarbazlde) was synthesized by one-pot synthesis method by pyridine-2-aldehyde, 4- (2-methylphenyl)-3-thiosemioarbazlde and Cd (NO3)2·4H2O. The structure of Cd (II) complex was characterized by single crystal X-ray diffraction. In the molecule, the Cd (II) ion is six-coordinated with four nitrogen atoms and two sulfur atoms of two pyridine-2-aldehyde-4- (2-methylphenyl)-3- thiosemioarbazlde ligands to form an distorted octahedral coordination geometry. The Cd (II) complex displays a 3D network structure by π-π interaction of benzene rings and pyridine rings of pyridine-2-aldehyde-4- (2-methylphenyl)-3-thiosemioarbazlde ligands.

The Crystal Structure of 2-Amino-4-Hydroxy-6- Methylpyrimidine-Trihydrate

The crystal structure of 2-amino-4-hydroxy-6-methylpyrimidine-trihydrate was characterized by single crystal X-ray diffraction. The crystal data: C10H20O5N6, triclinic, P-1, a = 6.8770 (14) Å, b = 10.486 (2) Å, c = 11.320 (2) Å, V = 778.9 (3) Å3, Z = 2, Rgt = 0.0646, wRref (F2) = 0.2144, T = 293 (2) K. The title compound molecules form 1D chained structure by the interaction of hydrogen bonds. And the one-dimensional chains further form three-dimensional network structure by interactions of hydrogen bonds and pyrimidine rings.

Crystal structure, Hirshfeld surface analysis, inter-action energy and DFT studies of (2Z)-2-(2,4-di-chloro-benzyl-idene)-4-nonyl-3,4-di-hydro-2H-1,4-benzo-thia-zin-3-one.

The title compound, C24H27Cl2NOS, contains 1,4-benzo-thia-zine and 2,4-di-chloro-phenyl-methyl-idene units in which the di-hydro-thia-zine ring adopts a screw-boat conformation. In the crystal, inter-molecular C-HBnz⋯OThz (Bnz = benzene and Thz = thia-zine) hydrogen bonds form chains of mol-ecules extending along the a-axis direction, which are connected to their inversion-related counterparts by C-HBnz⋯ClDchlphy (Dchlphy = 2,4-di-chloro-phen-yl) hydrogen bonds and C-HDchlphy⋯π (ring) inter-actions. These double chains are further linked by C-HDchlphy⋯OThz hydrogen bonds, forming stepped layers approximately parallel to (012). The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯H (44.7%), C⋯H/H⋯C (23.7%), Cl⋯H/H⋯Cl (18.9%), O⋯H/H⋯O (5.0%) and S⋯H/H⋯S (4.8%) inter-actions. Hydrogen-bonding and van der Waals inter-actions are the dominant inter-actions in the crystal packing. Computational chemistry indicates that in the crystal, C-HDchlphy⋯OThz, C-HBnz⋯OThz and C-HBnz⋯ClDchlphy hydrogen-bond energies are 134.3, 71.2 and 34.4 kJ mol-1, respectively. Density functional theory (DFT) optimized structures at the B3LYP/6-311 G(d,p) level are compared with the experimentally determined mol-ecular structure in the solid state. The HOMO-LUMO behaviour was elucidated to determine the energy gap. The two carbon atoms at the end of the nonyl chain are disordered in a 0.562 (4)/0.438 (4) ratio.

Improving cesium removal to clean-up the contaminated water using modified conjugate material

Crown ether based conjugate material was enabling the high functionality for stable complexation mechanism with cesium (Cs) and attracted the scientific community for potential real radioactive contaminated water treatment. This study was focused on ligand anchored conjugate material for radioactive Cs disposal based on adsorption techniques from nuclear liquid waste in Fukushima with high selectivity. A macrocyclic ligand of acetyl dibenzo-20-crown-6-ethers (AcDB20C6) was synthesized and directly embedded onto mesoporous inorganic silica. The Cs adsorption behavior was carried out with batch equilibrium techniques. The affecting experimental parameters such as solution pH, contact time, initial Cs concentration and competitive adsorption of Na and K ion concentrations were measured and optimized systematically. The sensitive pH range for high Cs removal was with broad range of 5.5–9.0, and the maximum adsorption capacity was 65.06 mg/g by the material at pH 7.0. The results clarified that conjugate material was high selectivity towards Cs even in the presence of a high level of Na and K ions rather than inorganic adsorbent because of the possible Cs-π interaction of the benzene ring from the crown ether ligand. The material was successfully investigated for radioactive Cs disposal for the potential treatment in Fukushima in the connection of in nuclear contaminated water treatment. The adsorbed Cs was desorbed with the eluent of 0.20 M HCl and then simultaneously regenerated at the same into the initial form for the next disposal operation after washing with water. The conjugate material was kept high functionality even in several cycles during adsorption–elution–regeneration processes. Then the proposed material could be used as promising material for selective radioactive Cs disposal from contaminated water in Fukushima, Japan.

Constructing a 3D-layered energetic metal–organic framework with the strong stacking interactions of hydrogen-bridged rings: the way to an insensitive high energy complex

Constructing 3D-layered EMOFs with strong stacking interactions of hydrogen-bridged rings to enhance their packing efficiency and energetic performances.

The remarkable propensity for the formation of C–H⋯π(chelate ring) interactions in the crystals of the first-row transition metal dithiocarbamates and the supramolecular architectures they sustain

C–H⋯π(chelate ring) interactions play an important role in assembling first-row transition metal dithiocarbamates in their crystals.