Bent Molecules Research Articles

(E)-N′-(2-Chlorobenzylidene)-1-methyl-4-nitro-1H-pyrrole-2-carbohydrazide

In the title compound, C13H11ClN4O3, the phenyl and pyrrolyl ring are linked by an ac­yl–hydrazone (R 2C=N—N—CO—R) group, forming a slightly bent mol­ecule: the dihedral angle subtended by the the phenyl and pyrrolyl rings is 8.46 (12)°. In the crystal, the three-dimensional supra­molecular structure is assembled by N—H⋯O hydrogen bonding. Mol­ecular sheets are formed parallel to (101) in a herringbone arrangement by weak van der Waals inter­actions; weak π–π [centroid–centroid phen­yl–phenyl and pyrrol­yl–pyrrolyl distances of 3.7816 (3) and 3.8946 (2) Å, respectively] inter­actions occur between neighbouring sheets.

Alignment and alignment transition of bent core nematics

We report on the alignment of nematics consisting of bimesogen bent core molecules of chlorine substituent of benzene derivative and their binary mixture with rod like nematics. It was found that the alignment layer made from polyimide material, which is usually used for promoting vertical (homeotropic) alignment of rod like nematics, promotes instead a planar alignment of the bent core nematic and its nematic mixtures. At higher concentration of the rod like nematic component in these mixtures, a temperature driven transition from vertical to planar alignment was found near the transition to isotropic phase.

Synthesis and mesomorphic behaviour of achiral four-ring unsymmetrical bent-core liquid crystals: Nematic phases

Achiral four ring unsymmetrical bent-core liquid crystals derived from 3-amino-2-methylbenzoic acid have been designed and synthesized with an imine, ester and photochromic azo linking moieties. These hockey-stick shape resembling bent molecules possess an alkoxy chain at one end of the molecule and methyl or methoxy group at the other end. The synthesis, phase transition temperatures and characterization of phase behaviour are discussed. The molecular structure characterization is consistent with data from elemental and spectroscopic analysis. The materials thermal behaviour and phase characterization have been investigated by differential scanning calorimetry and polarizing optical microscopy. All these compounds exhibit enantiotropic nematic phase over wide temperature range. Stable supercooling of nematic phase has been observed in methoxy homologues. The density functional theory (DFT) calculations were performed to obtain the stable molecular conformation, polarizability, dipole moment, Highest occupied molecular orbital (HOMO), Lowest unoccupied molecular orbital (LUMO) energies and bending angle of the compound.

Solvent‐Induced Crystalline‐State Emission and Multichromism of a Bent π‐Surface System Composed of Dibenzocyclooctatetraene Units

All bent out of shape: The solvent of crystallization effectively enhances the emission of flexible, bent, π-conjugated molecules in the crystalline state owing to control of the packing of the molecules in the structure. Multichromism such as thermochromism and vapochromism also arises from the solvent-controlled packing. This crystalline-state emission is attributable to the flexibility of cyclooctatetraene units of the bent π-conjugated molecules in the solid state (see figure).

Viscoelasticity, dielectric anisotropy, and birefringence in the nematic phase of three four-ring bent-core liquid crystals with an L-shaped molecular frame

Molecular shape is an important factor in determining the material properties of thermotropic liquid crystals (LCs). We synthesized and investigated several LC compounds formed by asymmetrically bent molecules with a rigid four-ring core in the shape of the letter ‘L’. We measured the temperature dependencies of dielectric permittivities, birefringence, splay K1 and bend K3 elastic constants, splay viscosity ηsplay and flow viscosities η|| and η⊥. The bend–splay anisotropy δK31 = K3 − K1 is negative, similar to the case of nematic LCs formed by symmetrically bent molecules of V-shape. The dielectric anisotropy Δe and birefringence are positive in the entire nematic range. The splay viscosity ηsplay and the flow viscosities η|| and η⊥ are smaller than the viscosities measured for the symmetric V-shaped bent-core materials at similar temperatures. The ratio Γ = ηsplay/η||,⊥ is in the range 5–4 that is typical for rod-like LCs. The reported L-shaped bent-core nematic LCs combine the useful features of bent-core LCs (such as a negative δK31, suitable for formulation of broad-range blue phases) with the relatively low viscosities, a property typical for rod-like LCs and beneficial for electro-optic switching applications.

Pyridinium and imidazolium 1,3,4-oxadiazole ionic liquid crystals: a thermal and photophysical systematic investigation

In this study we present the synthesis and complete structural characterization of twenty five 1,3,4-oxadiazole molecules (ionic and non-ionic) with some systematic structural variations, such as number of counterions, number of alkoxy chains, alkyl chain size, type of counterion and its position on the molecule. The thermal and photophysical properties for all compounds were investigated allowing a complete and interesting simultaneous study of the effect of structural changes on these properties. We show that every parameter studied affected both the thermal and photophysical properties. For these bent core molecules, the liquid crystalline behavior was observed only for compounds containing one counterion, SmA (monolayer or bilayer) being the predominant phase. The neutral (non-ionic) compounds and the imidazolium derivatives showed emission at around 360 nm and a high quantum yield, while most of the pyridinium derivatives showed emission at around 530 nm, a low quantum yield and a complex photophysical behavior. In all cases, the quantum yield for the different counterions follows the sequence ClO4− > BF4− > DS− > NO3− > Br−(I−).

Quasi-one-dimensional (Q1D) organic Mott insulators based on bent donor molecule EDO-EDSe-TTFVS

A series of conducting quasi-one-dimensional (Q1D) cation radical salts based on a bent donor molecule EDO-EDSe-TTFVS (1), 12ClO4, 12PF6(PhCl)0.25, and 12AsPF6(PhCl)0.25, were obtained via electrocrystallization. These salts show the semiconducting behavior with moderate conductivities up to 4.0Scm−1 and relatively large magnetic susceptibilities of 9×10−4emumol−1. The temperature dependent magnetic susceptibilities of these salts can be well fitted by the one-dimensional Heisenberg antiferromagnetic chain model. In their crystal structures, two donor molecules are crystallographically independent, while they are in the same oxidation state of +0.5 judging from their CC double bond lengths. The donor molecules form columnar stacks composed of donor dimers, and the size of the counter ion plays an important role on the degree of donor molecule dimerization. The electronic bands of these salts substantially split into the upper and lower two bands, and the upper bandwidth (WU) is smaller than on-site Coulomb repulsion of donor dimer (Udimer), WU/Udimer<0.85. These salts are intrinsically Mott insulators.

A new family of four-ring bent-core nematic liquid crystals with a highly polar end-group

A new family of four-ring achiral bent-core compounds derived from 2-methyl 3-amino benzoic acid with the methyl group in the bent direction incorporated into the central core have been designed and synthesised. These compounds possess an alkoxy chain attached at only one end of the bent core molecule, while the other arm consists of a biphenyl moiety possessing a highly polar cyano-group. The molecular structure has been confirmed by elemental analysis and spectroscopic data, and the thermal behaviour and phase characterisation has been investigated by differential scanning calorimetry and polarising microscopy. All the compounds exhibit a wide-range enantiotropic nematic phase. A comparison with non-mesomorphic unsubstituted and 4-methyl-substituted homologues is also presented.

Structures and physical properties of magnetic organic conductors based on bent donor molecule EDT-EDSe-TTFVS

The preparation, crystal structures, and physical properties of magnetic organic conductors based on a new bent donor molecule ethylenedithio-ethylenediseleno-tetrathiafulvalene-thioquinone-1,3-dithiolemethide (EDT-EDSe-TTFVS 3) are reported. The single crystals of 32FeCl4(EtOH) and 32FeBr4 are obtained by the electrochemical oxidation of 3 in the presence of (n-Bu4N)FeX4 (X=Cl, Br) at 45°C. Semiconducting behavior is observed with moderate conductivities of 4.0 and 0.6Scm−1 for 32FeCl4(EtOH) and 32FeBr4, respectively. In the crystal structures of both salts, the donor molecules and magnetic FeX4− ions form segregated layers. Within the organic layer, the donor molecules form columnar stacks, and the intra-columnar intermolecular overlap integrals are larger than the inter-columnar ones, resulting in the quasi one-dimensional electronic structures. There are atomic close contacts between the donor and FeX4 ion layers, which gives rise to the antiferromagnetic interaction of Fe(III) d-spins in both salts. Moreover, the Fe(III) d-spins in 32FeBr4 are subject to the antiferromagnetic ordering at 5K due to the strong π–d and d–d interactions.

Self-Organization of Bent Rod Molecules into Hexagonally Ordered Vesicular Columns

Bent-shaped rigid-core molecules with flexible chiral dendrons grafted to the outer side of the bend were synthesized and characterized by circular dichroism, differential scanning calorimetry, X-ray scatterings, and transmission electron microscopy in solution and the solid state. The bent aromatic rods based on hepta- and nonaphenylene with nitrile groups at both ends self-assemble into well-ordered hollow tubular structures in aqueous solution, while the bent rod based on heptaphenylene without nitrile groups showed no apparent aggregations in aqueous solution. In the solid state, the rigid-flexible molecules based on heptaphenylene rod without the nitrile group self-assemble into a 2D oblique columnar structure with the columnar cross-section containing two interlocked molecules. Remarkably, the rigid flexible molecules based on hepta-, nona-, and undecaphenylene with nitrile groups self-assemble into a hexagonal columnar structure with weak 3D order. A model of vesicular channel structure is proposed based on small- and wide-angle X-ray diffraction on oriented fibers, density measurement, reconstruction and simulation of electron density maps, and molecular dynamics simulation. In contrast to the hollow tubular structure found in solution, in the solid both the outside and the interior of the columns are filled by the pendant aliphatic coils. Filling of the interior of these vesicular channels is made possible by some bent rod molecules turning their obtuse apex inward. One in 7, 2 in 8, and 4 in 10 molecules are thus inverted in a column slice in compounds with hepta-, nona-, and undecaphenylene cores, respectively. These are new examples of vesicular double-segregated columnar structures recently discovered in some dendrons.

Winding single-molecule double-stranded DNA on a nanometer-sized reel

A molecular system of a nanometer-sized reel was developed from F1–ATPase, a rotary motor protein. By combination with magnetic tweezers and optical tweezers, single-molecule double-stranded DNA (dsDNA) was wound around the molecular reel. The bending stiffness of dsDNA was determined from the winding tension (0.9–6.0 pN) and the diameter of the wound loop (21.4–8.5 nm). Our results were in good agreement with the conventional worm-like chain model and a persistence length of 54 ± 9 nm was estimated. This molecular reel system offers a new platform for single-molecule study of micromechanics of sharply bent DNA molecules and is expected to be applicable to the elucidation of the molecular mechanism of DNA-associating proteins on sharply bent DNA strands.

Switching performance of a polymer-stabilized antiferroelectric liquid crystal based on bent-core molecules

Mixtures of a non-reactive and a photo-reactive liquid crystal, both consisting of bent core molecules, were used to prepare polymer-stabilized antiferroelectric liquid crystal cells by in-situ photo-polymerization. The mixtures exhibit a larger temperature range of the antiferroelectric phase than the pure compounds. The polymer network improves the ability of uniform alignment and thus enhances the switching contrast. In addition, the polymer-network reduces the switching times, in particular the relaxation time from the field-induced state to the ground state.

Vibrational spectra and tripartite entanglement in hydrogen sulfide

In this Brief Report an improved u(2) algebraic model is proposed to study both stretching and bending vibrational spectra of a bent triatomic molecule. The model with fewer parameters is used to reproduce the observed spectra of hydrogen sulfide (H${}_{2}$S) with better precision than the u(4) algebraic model. Furthermore, the tripartite entanglement dynamics is investigated for vibrationally localized states in H${}_{2}$S. It is shown that the entanglement of a highly excited state in the bending mode displays better quasiperiodicity than that in the stretch. Those are useful for molecular vibrations and multipartite quantum entanglement.

Notable formation of a cubic phase from small bent-angle molecules based on the 1,7-naphthalene central core and alkylthio tails

The mesomorphic properties of small angle, bent-shaped molecules [N(1,7)-S-n] consisting of a 1,7-naphthalene central core, typical Schiff-base side wings, and alkylthio tails with the carbon number n have been investigated, and a notable formation of a cubic (Cub) phase in addition to a distinct hexagonal columnar (Colh) phase was observed. The Cub phase can form when the terminal chain length is longer than 22 and is stable over a wider temperature range (25 °C) as the length increases up to 30. The space symmetry of the Cub phase was determined as Pmn with a lattice size of 160–170 A regardless of the terminal chain length. Assuming that the cubic unit cell is composed of a spherical assembly with a spatial electron density distribution, it can be described as containing eight spheres, each having a radius of 53 A and comprising 300 molecules. This formation of a novel Cub phase, like the micellar assembly phases, was understood as an enclosed layer formation caused by layer deformation with significant curvature resulting from the asymmetric packing of bent molecules in combination with the longer alkylthio tail groups of N(1,7)-S-n. It is noteworthy that the present observation of a Cub phase with unequivocal experimental evidence establishing both its lattice structure and size is the first example of a novel self-assembly mode in a bent-core liquid crystal (LC) molecular system.

Study of the vibrational spectra of bent XYZ molecule: An algebraic approach

In this work, we report a rigorous and detailed study of the vibrational spectra of some bent XYZ molecules like ONCl, HOCl, HOF, HOBr and HOI using the algebraic model. It has been shown in this study that the molecules ONCl, HOCl, HOF, HOBr, HOI and other similar bent XYZ molecules can be approximated very well using the algebraic approach in the strict local limit.

To Mix or Not To Mix: 2D Crystallization and Mixing Behavior of Saturated and Unsaturated Aliphatic Primary Amides

Physisorbed monolayers based on relatively weak noncovalent interactions can serve as excellent model systems for understanding crystallization of materials in reduced dimensionality. Here we employ a powerful combination of scanning tunneling microscopy (STM), differential scanning calorimetry (DSC), and computational modeling to reveal two-dimensional (2D) crystallization and mixing behavior of saturated and unsaturated (cis as well as trans) aliphatic primary amides. The foundation of the present work is laid by DSC measurements, which reveal characteristic adsorption and mixing behavior of aliphatic amides. These results are further supported by STM visualization of the adlayers. STM reveals, at submolecular resolution, the adsorption as well as the two-component 2D phase behavior of these molecules at the liquid-solid interface. The saturated and trans-unsaturated amides exhibit random mixing in view of their size and shape complementarity. Binary mixtures of saturated and cis-unsaturated amides, on the other hand, display unprecedented mixing behavior. The linear saturated and bent cis-unsaturated amide molecules are found to mix surprisingly better at the liquid-solid interface than might have been expected on account of the dissimilarity in their shapes. Strong, directional intermolecular hydrogen-bonding interactions as well as the relative stabilization energies of the adlayers are responsible for such unusual mixing behavior. Computational modeling provides additional insight into all the possible interactions in 2D assemblies and their impact on stabilization energies of the supramolecular networks. This study provides a model for understanding the effect of nanoscale cocrystallization on the thin film structure at interfaces and demonstrates the importance of molecular geometry and hydrogen bonding in determining the coadsorption behavior.

An approach to global rovibrational analysis based on anharmonic ladder operators: Application to Hydrogen Selenide [formula omitted

An algebraic approach to perform global rovibrational analysis of molecular spectra is presented. The approach combines the one-dimensional limit of the vibron model with rotational degrees of freedom. The model is based on the expression of the phase space Hamiltonian in terms of anharmonic ladder operators and the use of a symmetry-adapted basis set given by the linear combination of products of local vibrational and rotational wavefunctions. As an example we model the rovibrational spectra of a bent triatomic molecule, providing a global analysis for vibrational bands up to polyad 12 and J max = 5 of Hydrogen Selenide (H 2Se). Satisfactory fits of vibrational and rovibrational energies are obtained. A prediction of 2579 rovibrational energies up to J ⩽ 5 and polyad 12 for the 140 lowest vibrational bands is also obtained. A possible extension of the model to reach spectroscopic quality results in larger molecular systems is also given.

Switchable Columnar Phase Formed from Bent-Shaped Molecules with Low Bent-Angle Naphthalene Central Core and Alkylthio Tail

Novel low-angle bent molecules with 1,7-naphthalene central core and alkylthio tails form the hexagonal columnar phase as well as the well-known B4 phase. The columnar phase has a large two-dimensional hexagonal lattice of 65–70 Å and exhibits the antiferroelectric switching with the spontaneous polarization along the column axis. The column is considered to be constructed by the cylindrically enclosed layer.

Matrix Infrared Spectroscopy and a Theoretical Investigation of SUO and US2

AbstractUS2 and SUO molecules have been prepared by laser ablation of the solid materials and reaction of the elements during condensation in solid argon, which give the same absorptions as earlier U atom reactions with sulfur vapor and sulfur dioxide. The antisymmetric stretching mode of US2 shifts from 438.7 cm–1 in solid argon to 442.3 cm–1 in solid neon, which shows that the same electronic state is trapped in both matrix environments. Density functional calculations find a bent (3B2) ground state for the US2 molecule, and CASSCF/CASPT2 calculations reveal a multiconfigurational mixture of (5fφ)1(5fδ)1‐type states, whereas the most stable state for UO2 is a linear structure of the (5fφ)(7s) type. The bent triplet ground state SUO molecule exhibits similar multireference character with the U–O stretching mode at 857.1 cm–1 in solid argon. The linear SUO molecule computed at the CASPT2 level is only 2 kcal/mol above the bent structure. A detailed analysis of the bonding in US2 and SUO is provided and compared to the better known UO2 molecule.

ParaDock: a flexible non-specific DNA--rigid protein docking algorithm

Accurate prediction of protein–DNA complexes could provide an important stepping stone towards a thorough comprehension of vital intracellular processes. Few attempts were made to tackle this issue, focusing on binding patch prediction, protein function classification and distance constraints-based docking. We introduce ParaDock: a novel ab initio protein–DNA docking algorithm. ParaDock combines short DNA fragments, which have been rigidly docked to the protein based on geometric complementarity, to create bent planar DNA molecules of arbitrary sequence. Our algorithm was tested on the bound and unbound targets of a protein–DNA benchmark comprised of 47 complexes. With neither addressing protein flexibility, nor applying any refinement procedure, CAPRI acceptable solutions were obtained among the 10 top ranked hypotheses in 83% of the bound complexes, and 70% of the unbound. Without requiring prior knowledge of DNA length and sequence, and within <2 h per target on a standard 2.0 GHz single processor CPU, ParaDock offers a fast ab initio docking solution.