V-shaped Molecule Research Articles

New Al-MOFs based on sulfonyldibenzoate ions: a rare example of intralayer porosity.

A new sulfone-functionalized metal-organic framework [Al(OH)(SDBA)]·0.25DMF, denoted CAU-11, was synthesized using a V-shaped linker molecule 4,4'-sulfonyldibenzoic acid (H2SDBA). The crystal structure was solved from synchrotron X-ray powder diffraction data. Chains of trans corner-sharing AlO6 octahedra are interconnected by the carboxylate groups to form layers (ABAB stacking). Within the layers, hydrophobic lozenge-shaped pores with a diameter of 6.4 × 7.1 Å(2) are present inducing permanent porosity (aBET = 350 m(2) g(-1) and Vmicro = 0.17 cm(3) g(-1)). With the application of HT-methods (HT = high throughput), the isoreticular carboxylate functionalized compound [Al(OH)(H2DPSTC)]·0.5H2O (CAU-11-COOH) was synthesized using the linker molecule 3,3',4,4'-diphenylsulfonetetracarboxylic dianhydride (DPSDA), which hydrolyzes under the reaction conditions. Due to the additional noncoordinating carboxylic acid groups the pores are hydrophilic. Changing the molar ratio of Al(3+) to linker lead to the discovery of a second new compound [Al2(OH)2(DPSTC)(H2O)2]·0.5H2O (CAU-12). In CAU-12 the linker molecule is fully deprotonated which leads to different connectivity compared to the structure of CAU-11-COOH. Thermal activation of CAU-12 leads to dehydration and transformation of the structure to [Al2(OH)2(DPSTC)]·nH2O (CAU-12-dehy). Coordinated water molecules were removed, and the coordination site is replaced by the previously noncoordinating O atom of the adjacent carboxylate group. The SO2-groups point into the pores resulting in a highly hydrophobic three-dimensional framework. The compounds exhibit high thermal stability in air at least up to 420 °C. Synthesis of CAU-11 can be easily scaled up in very high yields (98%).

Highly efficient and practical resolution of 2,3:6,7-dibenzobicyclo[3.3.1]nona-2,6-diene-4,8-dione and stereoselective synthesis of its chiral diamine derivatives

The rigid V-shaped molecule (±)-4 could be efficiently resolved by commercially available BINOL in high enantiomeric excesses.

Phase control of the group velocity in a quantum-dot molecule

Absorption and dispersion properties of a V-shaped quantum-dot molecule are investigated. The effect of decay-induced interference and inter-dot tunneling on phase control of the absorption and the dispersion is then discussed. We find that in the presence of decay-induced interference or inter-dot tunneling the group velocity of a light pulse is completely phase dependant. The required switching times for switching the group velocity of a light pulse from subluminal to superluminal pulse propagation is then discussed.

Mechanistic insights into the role of Hop2-Mnd1 in meiotic homologous DNA pairing

The Hop2–Mnd1 complex functions with the DMC1 recombinase in meiotic recombination. Hop2–Mnd1 stabilizes the DMC1-single-stranded DNA (ssDNA) filament and promotes the capture of the double-stranded DNA partner by the recombinase filament to assemble the synaptic complex. Herein, we define the action mechanism of Hop2–Mnd1 in DMC1-mediated recombination. Small angle X-ray scattering analysis and electron microscopy reveal that the heterodimeric Hop2–Mnd1 is a V-shaped molecule. We show that the protein complex harbors three distinct DNA binding sites, and determine their functional relevance. Specifically, the N-terminal double-stranded DNA binding functions of Hop2 and Mnd1 co-operate to mediate synaptic complex assembly, whereas ssDNA binding by the Hop2 C-terminus helps stabilize the DMC1-ssDNA filament. A model of the Hop2-Mnd1-DMC1-ssDNA ensemble is proposed to explain how it mediates homologous DNA pairing in meiotic recombination.

First Keto-Functionalized Microporous Al-Based Metal–Organic Framework: [Al(OH)(O2C-C6H4-CO-C6H4-CO2)

Based on the V-shaped linker molecule 4,4'-benzophenonedicarboxylic acid, the new carbonyl-functionalized metal-organic framework (MOF) [Al(OH)(O(2)C-C(6)H(4)-CO-C(6)H(4)-CO(2))], denoted as CAU-8, was discovered employing high-throughput methods. The compound is obtained from 4,4'-benzophenonedicarboxylic acid, Al(2)(SO(4))(3)·18H(2)O in a mixture of N,N-dimethylformamide (DMF) and water under solvothermal conditions. The structure was determined from single-crystal X-ray diffraction data (I4(1)/a, a = b = 13.0625(5), c = 52.565(2) Å). The framework is based on infinite inorganic building units of trans-connected, corner-sharing AlO(6)-polyhedra. Parallel Al-O-chains are arranged in layers perpendicular to [001]. Within a layer an interchain distance of ∼1.1 nm is observed. The orientation of the Al-O-chains within neighboring layers is perpendicular to each other, along [100] and [010], respectively, and an ABCDA stacking of these layers is observed. The interconnection of these orthogonally oriented chains by the V-shaped dicarboxylate ions results in the formation a three-dimensional framework structure containing one-dimensional channels with a diameter of about 8 Å. The pore walls are lined by the keto-groups. CAU-8 was thoroughly characterized by X-ray powder diffraction (XRPD), thermogravimetric measurements, IR- and Raman-spectroscopy, elemental analysis, and gas sorption experiments using N(2) and H(2) as adsorptives. CAU-8 is stable up to 350 °C in air and exhibits a moderate porosity with a specific surface area of S(BET) = 600 m(2)/g and a micropore volume of 0.23 cm(3)/g. Moreover, a detailed topological analysis of the framework was carried out, and an approach for the topological analysis of MOFs based on infinite 1-periodic building units is proposed.

Recognition between V- and dumbbell-shaped molecules

A series of 2,6-bis(imino)pyridyl-based V-shaped compounds bearing various para-substituents on the terminal aromatic rings [C5H3N(CHN–C6H4R)2; R = OMe, iPr, Me, H, Cl, F, and CF3] have been prepared and investigated for their reversible binding with the dumbbell-shaped cations NH2+–{CH2–C6H3(OMe-3,5)2}2 and 9-anthryl–CH2–NH2+–CH2–C6H3(OMe-3,5)2. Three crystalline V-shaped compounds and a dumbbell hexafluorophosphate were characterised in the solid state by X-ray structural analysis. The binding mode of the 1 : 1 V-shaped molecule·dumbbell complexes was evaluated by 1H NMR spectroscopy. The binding constants (90–400 M−1 in dichloromethane) and stoichiometries of the complexes were determined using the Method of Continuous Variations and the Rose-Drago Method based on 1H NMR spectroscopic data. In a series of V-shaped compounds, the binding strength with both dumbbell cations diminishes with the decreasing electron-donating ability of the R substituents. Specifically, one of the diimine V-shaped compounds shows a stronger binding with the symmetrical dumbbell than with the unsymmetrical anthracene-containing dumbbell. Fluorescence measurements of equimolar mixtures of the V-shaped compounds and the unsymmetrical dumbbell have revealed a reduced anthracene emission which is approximately 50% that of the original intensity. Rapid and complete dissociation (<5 min) of the V-shaped compounds from the dumbbells was realised using an excess of acid or base, whereas only partial dissociation of the complexes was achieved with a large excess of water (<1 h).

Structures, Sorption Characteristics, and Nonlinear Optical Properties of a New Series of Highly Stable Aluminum MOFs

Employing high-throughput methods, the synthesis conditions for a series of six new MOFs based on aluminum ions and the V-shaped linker molecule 1,3-benzene dicarboxylic acid, denoted as CAU-10-X (CAU = Christian-Albrechts-University) with the sum formula [Al(OH)(C8H3O4X)]·solvent, were established (X = functional group in 5-position of the aromatic ring; X = H (1), CH3 (2), OCH3 (3) NO2 (4), NH2 (5), or OH (6)). Because of the absence of macroscopic crystals, the obtained compounds were structurally characterized employing XRPD-methods. The crystal structures of 1, 2, and 3 were refined using Rietveld methods. Although the described MOFs are isoreticular, they crystallize in several, sometimes noncentrosymmetric space groups (1, 4, 6), because of slight structural changes induced by the functionalization. These space groups were confirmed with second-harmonic generation measurements. All compounds are highly stable as confirmed by temperature-dependent XRPD and IR experiments and decompose at temperature...

Anti-Cancer Targeting Telomerase Inhibitors: &amp;beta;-Rubromycin and Oleic Acid

Telomerase is a ribonucleoprotein complex that elongates telomeric DNA and appears to play an important part in the cellular immortalization of cancers. In the screening of potent inhibitors of human telomerase, several inhibitors have been discovered from natural and chemical sources. Some compounds potently inhibit the activity of human telomerase. Rubromycins and fatty acids such as β-rubromycin and oleic acid, respectively, were found to be inhibitors of human telomerase. The IC(50) values of β-rubromycin and oleic acid were 8.60 and 8.78 μM, respectively. A kinetic study revealed that these compounds competitively inhibited the activity of telomerase with respect to the substrate of the primer and dNTP. The energy-minimized three-dimensional structure of β-rubromycin and oleic acid was calculated and designed. The V-shaped curve and molecule length of 18.7-20.3 Å in these compound structures were suggested to be important for telomerase inhibition. The three-dimensional structure of the active site of telomerase (i.e., the binding site of the primer and dNTP substrate) might have a "pocket" that could "join" these compounds. These results appear to suggest a potential structure for the development of more potent inhibitors of human telomerase.

3,3,3′,3′-Tetramethyl-6,6′-bis[(pyridin-4-yl)methoxy]-1,1′-spirobiindane monohydrate

The asymmetric unit in the title compound, C33H34N2O2·H2O, consists of a V-shaped mol­ecule and a water mol­ecule to which it is hydrogen bonded. The angle between the mean planes of the two spiro-connected indane groups is 77.06 (5)°. The two five-membered rings of the indane groups have envelope conformations with the methyl­ene atoms adjacent to the spiro C atom forming the flaps. They have deviations from the mean plane of the other four atoms in the rings of 0.374 (4) and 0.362 (4) Å. In the crystal, molecules are linked to form inversion dimers via O—H⋯N hydrogen bonds involving the pyridine N atoms and the solvent water mol­ecule. The dimers are linked into a chain along the b axis by π–π stacking inter­actions between a pyridine ring and its centrosymmetrically related ring in an adjacent dimer. The centroid–centroid distance between the planes is 3.7756 (17) Å, the perpendicular distance is 3.4478 (11) Å and the offset is 1.539 Å.

Hydrogen exchange and proteolytic degradation of ribonuclease A. The local splitting of the native structure and the conformation of loop segments

The limited proteolytic sites or nicksites are present only in one of the five loops of the RNase A molecule. The splitted loop 15-23 connects two structural domains in the hinge region of the interdomain contacts of the V-shaped molecule. The other four loops are inside two domains, 64-71 and 112-115 in the domain I (1-19, 47-81, 102-106) and 36-42 and 88-95 in the domain II (20-46, 82-101). Because of enhanced chain flexibility of the splitted loop in the pH-dependent conformational isomerization, deformation of its structure is slighter under the influence of the intermolecular contacts in the crystal lattice and more significant changes occur in loop conformation at the formation of the 3D swapped dimer of the RNase A molecule. The proteolytic splitting of the 15-23 loop proceeds due to the local fluctuation of the native protein structure.

1,3-Bis(biphenyl-4-yl)-2,2-dibromo-3-oxopropyl acetate

In the title compound, C29H22Br2O3, the dihedral angles between the mean planes of the benzene rings within each biphenyl group are 26.7 (8) and 30.9 (8)°. The mean planes of the terminal and inner benzene rings of the biphenyl groups bonded through a propan-1-one group in the V-shaped mol­ecule are oriented at angles of 66.1 (7) and 60.0 (8)°, respectively. The two Br atoms are opposite the propen-1-one group. Weak inter­molecular C—H⋯O and C—H⋯π inter­actions are observed in the crystal structure.

Density-functional-theory investigation of conformations,C13shielding, and magnetic field interactions in a V-shaped phenylene bis carboxylate homologous series

Density functional theory (DFT) has been employed in a conformational study of a bent-core PBBC homologous series. IR spectra, GIAO-DFT chemical shielding tensors (CSTs), and molecular susceptibility tensors (MSTs) are theoretically calculated for various optimized conformations established by searching the potential energy surface of each PBBC V-shaped molecule. The IR results could aid the understanding of vibration normal modes, while the MST results can illuminate the alignment properties of the V-shaped molecules in an external magnetic field. CSTs of the aromatic carbons, and those previously measured by the 2D-NMR SUPER technique (with some (13)C NMR peaks reassigned for correctness based on new DFT calculations), were found to be in good agreement. These verified experimental CSTs are then used to revisit the (13)C NMR data to yield structural and local orientational order parameters for two members of the PBBC series. The PBBC series studied using the combined DFT-(13)C NMR approach strongly supports the notion that lesser populated conformational states found by DFT could be reached in the studied mesogens 10DClPBBC and 11ClPBBC upon decreasing temperature, as revealed by the change in the bend angle determined by NMR and identified with those of the DFT molecular structures optimized for various conformers.

对称Y型分子向列相液晶的相变

Based on the V-shaped molecule of biaxial nematic liquid crystal,a model of symmetric Y-shaped molecule is developed.In this model the Y-shaped molecule is Abstracted to three linked rod-like arms.Using a simple biaxial molecular interaction model in nematic liquid crystal,the interaction energy between two molecules is obtained by the superposition of all rod-to-rod interactions.With the mean field approximation,the free energy of the system is derived and the result shows that the free energy is the function of order parameters.The relationship between the Y-shaped molecule and its ability to form a biaxial nematic phase is established.And phase transitions from isotropic to uniaxial nematic(NI phase transition) and from uniaxial to biaxial nematic(IB phase transition) are obtained.

(3R,3aS,6R,6aR)-3-(1-Nitroethyl)perhydrofuro[3,2-b]furan-3,6-diol

The mol­ecule of the title compound, C8H13NO6, a sucrose derivative, consists of two fused tetra­hydro­furan rings having the cis arrangement at the ring junctions, giving a V-shaped mol­ecule. An intra­molecular O—H⋯O inter­action occurs. Inter­molecular O—H⋯O hydrogen bonds help to stabilize the crystal structure.

Biaxial phases of bent-core liquid crystal polymers in shear flows

We develop a kinetic theory of the biaxial phases for the bent-core or V-shaped liquid crystal polymer solution (VLCPS). The Brownian motion of the biaxial molecules, biaxial molecular excluded interaction, and the rotary convection are modeled explicitly. Using the hydrodynamic theory, we study the flow-driven orientational dynamics and the corresponding rheological response in selected regimes of plane shear flows, strength of intermolecular interaction, and the bent-angle of the molecule. We identify three steady state biaxial phases and three periodic motions at various regimes of the shear rate and strength of the intermolecular potential. Phase transition sequences among the orientational phases and motions are documented with respect to the strength of the intermolecular potential at fixed bent angles. The effect of the molecular configuration (or the bent- angle) of the V-shaped molecule on mesoscopic phases and their transition sequences is investigated as well.

X‐ray structure of Danio rerio secretagogin: A hexa‐EF‐hand calcium sensor

Many essential physiological processes are regulated by the modulation of calcium concentration in the cell. The EF-hand proteins represent a superfamily of calcium-binding proteins involved in calcium signaling and homeostasis. Secretagogin is a hexa-EF-hand protein that is highly expressed in pancreatic islet of Langerhans and neuroendocrine cells and may play a role in the trafficking of secretory granules. We present the X-ray structure of Danio rerio secretagogin, which is 73% identical to human secretagogin, in calcium-free form at 2.1-A resolution. Secretagogin consists of the three globular domains each of which contains a pair of EF-hand motifs. The domains are arranged into a V-shaped molecule with a distinct groove formed at the interface of the domains. Comparison of the secretagogin structure with the solution structure of calcium-loaded calbindin D(28K) revealed a striking difference in the spatial arrangement of their domains, which involves approximately 180 degrees rotation of the first globular domain with respect to the module formed by the remaining domains.

Propane-2,2-diyl di-p-phenylene dibenzoate

The V-shaped propeller-like mol­ecule of the title compound, C29H24O4, does not exhibit crystallographic twofold symmetry as the two benzene rings are twisted asymmetrically with respect to both the central propyl plane and the benzo­yloxy groups [4.6 (2), 43.6 (2)° and 45.07 (8), 69.50 (8)°]. In the crystal structure, centrosymmetrically related mol­ecules form a dimer through C—H⋯π inter­molecular inter­actions.

Ethyl 4-(2-chloro-4-nitrophenoxy)benzoate

The title compound, C15H12ClNO5, was synthesized by the reaction of ethyl 4-hydroxybenzoate and 1,2-dichloro-4-nitrobenzene in the presence of potassium hydroxide. In the V-shaped molecule, the dihedral angle between the two benzene rings is 72.90 (5)°.

Controlled formation and topologies of thiophenolate-based macrocycles: rings, cylinders and bowls

The Schiff-base condensations of 1,3-diaminopropane with a protected thiophenol dialdehyde in the presence of Ni(2+), Pd(2+) or Zn(2+) can be controlled to yield either mononuclear acyclic, or 2 + 2 and 4 + 4 macrocyclic complexes by the choice of both metal cation and counteranion. The Ni(2+) complex of the 2 + 2 macrocycle contains two square-planar nickel ions and shows an arrangement similar to one observed previously: the mu-S atoms of the thiophenolate groups are pyramidal and lie on the same side of the plane defined by the four N atoms of the macrocycle to give a V-shaped molecule. By contrast, the Zn(2+) complex of the 2 + 2 macrocycle undergoes oligomerization to yield a bowl-shaped hexanuclear complex that includes a mu(3)-carbonate anion. Essential for this topology is the presence of three mu(3)-S-thiophenolato groups that link the three macrocyclic units to form a Zn(3)S(3) ring that seals the bottom part of the bowl. In this arrangement, one of the pyramidal mu(3)-S atoms in each dinuclear Zn(2+) complex is inverted relative to the arrangement observed for the dinickel complexes. Molecular modelling suggests that inversion about the mu-S atoms of the 2 + 2 macrocyclic complexes is readily accessible at room temperature and that the contrasting arrangements observed for the Ni(2+) and Zn(2+) complexes are those energetically most favourable for the respective metal ions. Rare 4 + 4 macrocyclic complexes are isolated as neutral dinuclear complexes for Ni(2+) and Pd(2+) and as a tetranuclear complex cation for Zn(2+). The topologies of these systems contrast significantly: those with two square-planar Ni(2+) or Pd(2+) ions form extended rings, while that with Zn(2+) forms a sulfur-lined cylinder which hosts acetonitrile molecules in the crystalline state. Reaction conditions can also be optimised to produce 2 + 1 acyclic ligands as their mononuclear Ni(2+) and Pd(2+) complexes, providing potentially useful building blocks for production of more complicated macrocyclic and supramolecular systems.

Biaxial nematic phases and V-shaped molecules: A Monte Carlo simulation study

Inspired by recent claims that compounds composed of V-shaped molecules can exhibit the elusive biaxial nematic phase, we have developed a generic simulation model for such systems. This contains the features of the molecule that are essential to its liquid crystal behavior, namely the anisotropies of the two arms and the angle between them. The behavior of the model has been investigated using Monte Carlo simulations for a wide range of these structural parameters. This allows us to establish the relationship between the V-shaped molecule and its ability to form a biaxial nematic phase. Of particular importance are the criteria of geometry and the relative anisotropy necessary for the system to exhibit a Landau point, at which the biaxial nematic is formed directly from the isotropic phase. The simulations have also been used to determine the orientational order parameters for a selection of molecular axes. These are especially important because they reveal the phase symmetry and are connected to the experimental determination of this. The simulation results show that, whereas some positions are extremely sensitive to the phase biaxiality, others are totally blind to this.