Conformational polymorphism in a heteromolecular single crystal leads to concerted movement akin to collective rack-and-pinion gears at the molecular level

Stereoselective Solid-State Synthesis of Biologically Active Cyclobutane and Dicyclobutane Isomers via Conformation Blocking and Transference

Conformations in the solid state are typically fixed during crystallization. Transference of "frozen" C=C conformations in 3,5-bis((E)-2-(pyridin-4-yl)vinyl)methylbenzene (CH3-3,5-bpeb) by photodimerization selectively yielded cyclobutane and dicyclobutane isomers, one of which (Isomer 2) exhibited excellent in vitro anti-cancer activity towards T-24, 7402, MGC803, HepG-2, and HeLa cells.

A phase variety of fluorinated ionic liquids: Molecular conformational and crystal polymorph

Crystal polymorphs of fluorinated ionic liquids (fILs) were examined at low-temperature (LT) by Raman spectroscopy. The fILs were 1-alkyl-3-methylimidazolium perfluorobutanesulfonate, [C_nmim][PFBS] (n = 4, 6, and 8). The cations and anion possess conformational degrees of freedom. Various LT phases were derived from the conformational polymorphs of the cations and the anion. Conformational flexibility depended on alkyl chain length. The crystal polymorphs in the fILs were sensitive to molecular conformations and flexibility.

Emergence of Coupled Rotor Dynamics in Metal-Organic Frameworks via Tuned Steric Interactions

The organic components in metal–organic frameworks (MOFs) are unique: they are embedded in a crystalline lattice, yet, as they are separated from each other by tunable free space, a large variety of dynamic behavior can emerge. These rotational dynamics of the organic linkers are especially important due to their influence over properties such as gas adsorption and kinetics of guest release. To fully exploit linker rotation, such as in the form of molecular machines, it is necessary to engineer correlated linker dynamics to achieve their cooperative functional motion. Here, we show that for MIL-53, a topology with closely spaced rotors, the phenylene functionalization allows researchers to tune the rotors’ steric environment, shifting linker rotation from completely static to rapid motions at frequencies above 100 MHz. For steric interactions that start to inhibit independent rotor motion, we identify for the first time the emergence of coupled rotation modes in linker dynamics. These findings pave the way for function-specific engineering of gear-like cooperative motion in MOFs.

Toward an Understanding of the Formation and Desolvation of Methanol Solvate, and Structure of Methanolysis Product: A Case Study of Nicosulfuron

Nicosulfuron (NS) is a widely used sulfonylurea herbicide because of its high selectivity, broad spectrum of herbicide activity, and excellent performance. In this work, nicosulfuron methanol solvate (NS-MeOH) and [[3-[(Dimethylamino)carbonyl]-2-pyridinyl]sulfonyl]carbamic acid methyl ester (PCM) as a product of methanolysis of NS were obtained. Both of their structures were determined by a single crystal X-ray diffraction. A broad range of analytical techniques was applied to characterize the NS-MeOH, such as Powder X-ray diffraction (PXRD), thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), and hot stage microscopy (HSM). Combined with the analysis of the Independent gradient model (IGM), Atom-in-molecules (AIM), and Hirshfeld surface (HS), direct insights into the role of solvent played in the formation of NS-MeOH and the mechanism of solid-to-solid phase transformation of NS-MeOH could be obtained. In addition, the aqueous solubility of NS was improved through the formation of NS-MeOH. A systematic investigation of herbicidal activity of NS and PCM was carried out. It was found that NS and NS-MeOH had similar herbicidal activities at the experimental concentrations while PCM exhibited significantly lower activity. It was suggested that methanolysis of the sulfonylurea bridge in the NS molecule exerted a great influence on the herbicidal activity.

Regioselective Photochemical Cycloaddition Reactions of Diolefinic Ligands in Coordination Polymers

The pure diolefinic ligand 1,4-bis(pyridin-4-yl)-1,3-butadiene (bpbde) is photostable in the crystalline state. With the assistance of coordination-driven metal-organic assemblies, the photoreactivity of this diolefinic ligand can be significantly enhanced. A hydrothermal reaction of bpbde with Cd(NO₃ )₂ ⋅4 H₂ O and the auxiliary ligand adipic acid resulted in the formation of a two-dimensional photoreactive coordination polymer (CP), [Cd(adipate)(bpbde)]_n (1). When the aliphatic carboxylic acid was replaced by pimelic acid, another photoreactive CP [Cd(pimelate)(bpbde)]_n (2) with a three-dimensional framework was obtained. With irradiation of 365 nm UV light, the bpbde ligands in crystalline 1 and 2 underwent a regioselective photochemical [2+2] cycloaddition reaction and converted to 3,4,7,8-tetra(pyridin-4-yl)tricyclo[4.2.0.0^2,5 ]octane (tptco) and 1,3-bis(pyridin-4-yl)-2,4-bis(2-(pyridin-4-yl)vinyl)cyclobutane (bpbpvcb), respectively. The results provide an interesting insight into the rational design of highly regio- or stereoselective photocatalytic reactions for the formation of special organic molecules.

Assembling an alkyl rotor to access abrupt and reversible crystalline deformation of a cobalt(II) complex

Harnessing molecular motion to reversibly control macroscopic properties, such as shape and size, is a fascinating and challenging subject in materials science. Here we design a crystalline cobalt(II) complex with an n-butyl group on its ligands, which exhibits a reversible crystal deformation at a structural phase transition temperature. In the low-temperature phase, the molecular motion of the n-butyl group freezes. On heating, the n-butyl group rotates ca. 100° around the C–C bond resulting in 6–7% expansion of the crystal size along the molecular packing direction. Importantly, crystal deformation is repeatedly observed without breaking the single-crystal state even though the shape change is considerable. Detailed structural analysis allows us to elucidate the underlying mechanism of this deformation. This work may mark a step towards converting the alkyl rotation to the macroscopic deformation in crystalline solids.

Molecular motion can potentially be harnessed to control macroscopic properties such as size and shape. Here, the authors show that the phase transition of a cobalt(II) complex with an n-butyl group on its ligands, results in a reversible crystal deformation at the structural phase transition temperature.

Molecular motion, dielectric response, and phase transition of charge-transfer crystals: acquired dynamic and dielectric properties of polar molecules in crystals

Molecules in crystals often suffer from severe limitations on their dynamic processes, especially on those involving large structural changes. Crystalline compounds, therefore, usually fail to realize their potential as dielectric materials even when they have large dipole moments. To enable polar molecules to undergo dynamic processes and to provide their crystals with dielectric properties, weakly bound charge-transfer (CT) complex crystals have been exploited as a molecular architecture where the constituent polar molecules have some freedom of dynamic processes, which contribute to the dielectric properties of the crystals. Several CT crystals of polar tetrabromophthalic anhydride (TBPA) molecules were prepared using TBPA as an electron acceptor and aromatic hydrocarbons, such as coronene and perylene, as electron donors. The crystal structures and dielectric properties of the CT crystals as well as the single-component crystal of TBPA were investigated at various temperatures. Molecular reorientation of TBPA molecules did not occur in the single-component crystal, and the crystal did not show a dielectric response due to orientational polarization. We have found that the CT crystal formation provides a simple and versatile method to develop molecular dielectrics, revealing that the molecular dynamics of the TBPA molecules and the dielectric property of their crystals were greatly changed in CT crystals. The TBPA molecules underwent rapid in-plane reorientations in their CT crystals, which exhibited marked dielectric responses arising from the molecular motion. An order-disorder phase transition was observed for one of the CT crystals, which resulted in an abrupt change in the dielectric constant at the transition temperature.

Thermodynamic parameters of the pedal motion in the crystal structures of two bromomethylated azobenzenes

Differences in the thermodynamic parameters of the central N-atoms' pedal motion in two bromomethylated azobenzenes were determined by multi-temperature X-ray diffraction, and rationalized by packing studies.

Dynamics of a caged imidazolium cation–toward understanding the order-disorder phase transition and the switchable dielectric constant

A molecular compass-like behaviour is found in a perovskite-type cage compound (HIm)₂[KCo(CN)₆], leading to the switchable and anisotropic dielectric constants.

Molecular motor-driven abrupt anisotropic shape change in a single crystal of a Ni complex

Many molecular machines with controllable molecular-scale motors have been developed. However, transmitting molecular movement to the macroscopic scale remains a formidable challenge. Here we report a single crystal of a Ni complex whose shape changes abruptly and reversibly in response to thermal changes at around room temperature. Variable-temperature single-crystal X-ray diffraction studies show that the crystalline shape change is induced by an unusual 90° rotation of uniaxially aligned oxalate molecules. The oxalate dianions behave as molecular-scale rotors, with their movement propagated through the entire crystalline material via intermolecular hydrogen bonding. Consequently, the subnanometre-scale changes in the oxalate molecules are instantly amplified to a micrometre-scale contraction or expansion of the crystal, accompanied by a thermal hysteresis loop. The shape change in the crystal was clearly detected under an optical microscope. The large directional deformation and prompt response suggest a role for this material in microscale or nanoscale thermal actuators.

Synthon polymorphs of 1 : 1 co-crystal of 5-fluorouracil and 4-hydroxybenzoic acid: their relative stability and solvent polarity dependence of grinding outcomes

Two synthon polymorphs of 1 : 1 co-crystals of 5-fluorouracil and 4-hydroxybenzoic acid were synthesized, and the crystal structures were determined.

Thermally-induced phase transition of pseudorotaxane crystals: changes in conformation and interaction of the molecules and optical properties of the crystals

This paper presents a pseudorotaxane that acts as a thermally driven molecular switch in the single-crystal state. Crystals of the cationic pseudorotaxane consisting of dibenzo[24]crown-8 (DB24C8) and N-(xylylammonium)-methylferrocene as the cyclic and axle component molecules, respectively, undergo crystalline-phase transition at 128 °C with heating and 116 °C with cooling, according to differential-scanning-calorimetry measurements. X-ray crystallographic analyses revealed that the phase transition was accompanied by rotation of the 4-methylphenyl group of the axle component molecule and a simultaneous shift in the position of the PF(6)(-) counteranion. Crystalline phase transition changes the conformation and position of the DB24C8 molecule relative to the ammonium cation partially; the interaction between the cyclic component and the PF(6)(-) anion in the crystal changes to a greater extent. Moreover, there are changes in the vibration angle (θ) and birefringence (Δn) on the (001) face of the crystal transitionally; θ is rotated by +12°, and Δn is decreased from 0.070 to 0.059 upon heating across the phase transition temperature. The phase transition and accompanying change in the optical properties of the crystal occur reversibly and repeatedly upon heating and cooling processes. The switching rotation of the aromatic plane of the molecule induces a change in the optical anisotropy of the crystal, which is regarded as a demonstration of a new type of optical crystal. Partial replacement of the PF(6)(-) anion with the bulkier AsF(6)(-) anion forms crystals with similar crystallographic parameters. An increase in the AsF(6)(-) content decreases the reversible-phase-transition temperature gradually down to 99 °C (T(end)) and 68 °C (T(exo)) ([AsF(6)(-)]:[PF(6)(-)] = 0.4:0.6).

Crystalline molecular machines: function, phase order, dimensionality, and composition

The design of molecular machines is stimulated by the possibility of developing new materials with complex physicochemical and mechanical properties that are responsive to external stimuli. Condensed-phase matter with anisotropic molecular order and controlled dynamics, also defined as amphidynamic crystals, offers a promising platform for the design of bulk materials capable of performing such functions. Recent studies have shown that it is possible to engineer molecular crystals and extended solids with Brownian rotation about specific axes that can be interfaced with external fields, which may ultimately be used to design novel optoelectronic materials. Structure/function relationships of amphidynamic materials have been characterized, establishing the blueprints to further engineer sophisticated function. However, the synthesis of amphidynamic molecular machines composed of multiple "parts" is essential to realize increasingly complex behavior. Recent progress in amphidynamic multicomponent systems suggests that sophisticated functions similar to those of simple biomolecular machines may eventually be within reach.

Molecular recognition and self-assembly special feature: Encapsulated-guest rotation in a self-assembled heterocapsule directed toward a supramolecular gyroscope

The self-assembled heterocapsule 1.2, which is formed by the hydrogen bonds of tetra(4-pyridyl)-cavitand 1 and tetrakis(4-hydroxyphenyl)-cavitand 2, encapsulates 1 molecule of guests such as 1,4-diacetoxybenzene 3a, 1,4-diacetoxy-2,5-dimethylbenzene 3b, 1,4-diacetoxy-2,5-dialkoxybenzenes (3c, OCH(3); 3d, OC(2)H(5); 3e, OC(3)H(7); 3f, OC(4)H(9); 3g, OC(5)H(11); 3h, OC(6)H(13); 3i, OC(8)H(17)), 1,4-diacetoxy-2,5-difluorobenzene 4a, and 1,4-diacetoxy-2,3-difluorobenzene 4b. The X-ray crystallographic analysis of 3c@(1.2) showed that the acetoxy groups at the 1,4-positions of 3c are oriented toward the 2 aromatic cavity ends of 1.2 and that 3c can rotate along the long axis of 1.2. Thus, the 1.2 (stator) with the encapsulation guest (rotator) behaves as a supramolecular gyroscope. A variable temperature (VT) (1)H NMR study in CDCl(3) showed that 3a, 3b, 4a, and 4b within 1.2 rotate rapidly even at 218 K, whereas guest rotation is almost inhibited for 3h and 3i even at 323 K. In this respect, 4b with a large dipole moment is a good candidate for the rotator of 1.2. For 3c-3g, the enthalpic (DeltaH(double dagger)) and entropic (DeltaS(double dagger)) contributions to the free energy of activation (DeltaG(double dagger)) for the guest-rotational steric barriers within 1.2 were obtained from Eyring plots based on line-shape analysis of the VT (1)H NMR spectra. The value of DeltaG(double dagger) increased in the order 3c < 3d < 3e < 3f < 3g. Thus, the elongation of the alkoxy chains at the 2,5-positions of 3 puts the brakes on guest rotation within 1.2.

Molecular Solids from Symmetrical Bis(piperazine-2,5-diones) with Open and Closed Monomer Conformations

The design, synthesis and solid state structures of a new class of xylylene-linked bis(1,4- piperazine-2,5-diones) are reported in an effort to extend the molecular framework of piperazine-2,5-diones. These compounds were derived from piperazine-2,5-dione as the core structure, synthesized via a new efficient route, and their crystal structures were determined. We examined the effects of side chain substitution on conformations of the linked bis-DKPs. Crystallization of 3,3'-[1,4-phenylenebis(methylene)]-bis[6-(hydroxymethyl)-1,4-dimethylpiperazine-2,5-dione] yielded molecular solids with an unusual network of "C"-shaped monomers held together by four intermolecular hydrogen bonds per asymmetric unit. Similarly, intermolecular interactions between the iodomethyl groups in 3,3'-[1,4-phenylenebis(methylene)]-bis[6-(iodomethyl)-1,4-dimethyl-piperazine-2,5-dione] result in the monomers adopting a "C"-shape in the solid state. Assembly of the monomers with side chains converted to methyl groups or tert-butyldimethylsilyl ethers, thereby lacking these stabilizing intermolecular interactions, results in an infinite array of "S"-shaped conformations. These results suggest that the interplay between the attractive intermolecular interactions and repulsive steric interactions of the substituents at the C6 and C6' positions of the diketopiperazine rings is important in determining the solid-state conformations of xylylene-linked bis(piperazine-2,5-diones).

Self-organization, optical, and electrical properties of alpha-quinquethiophene-dinucleotide conjugates

The synthesis and properties of (5')TA(3')-t5 (8a) and (5')CG(3')-t5 (8b) conjugates, in which the self-complementary dinucleotides TA and CG are covalently bound to the central ring of alpha-quinquethiophene (t5), are described. According to molecular mechanics calculations, the preferred conformation of both 8a and 8b is that with the dinucleotide folded over the planar t5 backbone, with the nucleobases facing t5 at stacking distance. The calculations show that the aggregation process of 8a and 8b is driven by a mix of nucleobase-thiophene interactions, hydrogen bonding between nucleobases (non Watson-Crick (W&C) in TA, and W&C in CG), van der Waals, and electrostatic interactions. While 8b is scarcely soluble in any solvents, 8a is soluble in water, indicating that the aggregates of the former are more stable than those of the latter. Microfluidic-induced self-assembly studies of 8a showed the formation of lamellar, spherulitic, and dendritic supramolecular structures, depending on the concentration and solvent evaporation time. The self-assembled structures displayed micrometer dimensions in the xy plane of the substrate and nanometer dimensions in the z direction. Spatially resolved confocal microscopy and spectroscopy showed that the aggregates were characterized by intense fluorescence emission. Cast films of 8a from water solutions showed chirality transfer from the dinucleotide to t5. The hole mobility of the cast films of 8a was estimated using a two-electrode device under high vacuum and found to be up to two orders of magnitude greater than those previously measured for dinucleotide-quarterthiophene conjugates under the same experimental conditions.