Planar Conformation Research Articles

Use of Intramolecular 1,5-Sulfur-Oxygen and 1,5-Sulfur-Halogen Interactions in the Design of N-Methyl-5-aryl-N-(2,2,6,6-tetramethylpiperidin-4-yl)-1,3,4-thiadiazol-2-amine SMN2 Splicing Modulators.

Spinal muscular atrophy (SMA) is a debilitating neuromuscular disease caused by low levels of functional survival motor neuron protein (SMN) resulting from a deletion or loss of function mutation of the survival motor neuron 1 (SMN1) gene. Branaplam (1) elevates levels of full-length SMN protein in vivo by modulating the splicing of the related gene SMN2 to enhance the exon-7 inclusion and increase levels of the SMN. The intramolecular hydrogen bond present in the 2-hydroxyphenyl pyridazine core of 1 enforces a planar conformation of the biaryl system and is critical for the compound activity. Scaffold morphing revealed that the pyridazine could be replaced by a 1,3,4-thiadiazole, which provided additional opportunities for a conformational constraint of the biaryl through intramolecular 1,5-sulfur-oxygen (S···O) or 1,5-sulfur-halogen (S···X) noncovalent interactions. Compound 26, which incorporates a 2-fluorophenyl thiadiazole motif, demonstrated a greater than 50% increase in production of full-length SMN protein in a mouse model of SMA.

A Dynamic Substrate is Required for MhuD-Catalyzed Degradation of Heme to Mycobilin.

The noncanonical heme oxygenase MhuD from Mycobacterium tuberculosis binds a heme substrate that adopts a dynamic equilibrium between planar and out-of-plane ruffled conformations. MhuD degrades this substrate to an unusual mycobilin product via successive monooxygenation and dioxygenation reactions. This article establishes a causal relationship between heme substrate dynamics and MhuD-catalyzed heme degradation, resulting in a refined enzymatic mechanism. UV/vis absorption (Abs) and electrospray ionization mass spectrometry (ESI-MS) data demonstrated that a second-sphere substitution favoring the population of the ruffled heme conformation changed the rate-limiting step of the reaction, resulting in a measurable buildup of the monooxygenated meso-hydroxyheme intermediate. In addition, UV/vis Abs and ESI-MS data for a second-sphere variant that favored the planar substrate conformation showed that this change altered the enzymatic mechanism resulting in an α-biliverdin product. Single-turnover kinetic analyses for three MhuD variants revealed that the rate of heme monooxygenation depends upon the population of the ruffled substrate conformation. These kinetic analyses also revealed that the rate of meso-hydroxyheme dioxygenation by MhuD depends upon the population of the planar substrate conformation. Thus, the ruffled heme conformation supports rapid heme monooxygenation by MhuD, but further oxygenation to the mycobilin product is inhibited. In contrast, the planar substrate conformation exhibits altered heme monooxygenation regiospecificity followed by rapid oxygenation of meso-hydroxyheme. Altogether, these data yielded a refined enzymatic mechanism for MhuD where access to both substrate conformations is needed for rapid incorporation of three oxygen atoms into heme yielding mycobilin.

Synthesis, crystal structure, density functional theory, Hirshfeld surface analysis and molecular docking studies of 2-(2-phenylanthracen-9-yl)thiophene derivatives

Thiophene containing molecules have been distinguished as potential candidates in the largely emergent chemical world of heterocyclic compounds that show likely pharmacological characteristics. The knowledge of a mixture of synthetic pathways and the different physicochemical parameters of such compounds describe the especial interest of medicinal chemists to produce combinatorial collections and carry out in-depth efforts in the search of lead molecules. Among the various group of compounds studied, thiophene moieties stand out as unique in features due to their biological, pharmacological and medicinal properties. Synthesis, crystal structure, conformation and density functional theory of 2-(2-phenylanthracen-9-yl)thiophene derivative have been investigated in detail. Thiophene moiety are in planar conformation and having C-H…O type of hydrogen bonds and Van der Waals forces. Density functional theory has been applied to the thiophene derivative. Thiophene compounds score highly against the targeted protein and can be compared to the co-crystal ligand. Hirshfeld surface studies have been used to confirm and quantify the supramolecular features.

Selection of Planar Chiral Conformations between Pillar[5,6]arenes Induced by Amino Acid Derivatives in Aqueous Media.

Chiral α-amino acids play critical roles in the metabolic process in nearly all life forms. So far, chiral recognition of α-amino acids has mainly focused on the determination of l/d enantiomers. Herein, selection of planar chiral conformations between water-soluble pillar[5]arene WP5 and pillar[6]arene WP6 was observed due to α-side chain or ethyl ester moieties of l-α-amino acid ethyl ester hydrochlorides binding with WP5 and WP6, respectively. Therefore, α-side chain and ethyl ester moieties of l-α-amino acid ethyl ester hydrochlorides were recognized by observing the induced CD signal and its inversion. This is a rare example of being able to detect the chiral region around α-carbon of a chiral α-amino acid molecule.

Mechanism of Elastic Properties of Biodegradable Poly[(R)-3-Hydroxybutyrate-co-4-hydroxybutyrate] Films Revealed by Synchrotron Radiation.

Reversible elastic films of biobased and biodegradable poly[(R)-3-hydroxybutyrate-co-4-hydroxybutyrate] [P(3HB-co-4HB)] were prepared by uniaxial drawing procedures. Mechanical properties and highly ordered film structures were investigated by tensile testing and both static-state and in situ wide-angle X-ray diffraction and small-angle X-ray scattering with synchrotron radiation during stretching and relaxing. Despite the crystalline nature of the polymers, the elongation at break of these films was greater than 1500%. Reversible elasticity was achieved after the first 10 times of uniaxial stretching. X-ray measurement results indicated that on stretching, β-form molecular chains with a planar zigzag conformation were introduced from molecular chains with random coils in the amorphous regions between α-form lamellar crystals. Notably, the orientation of the α-form lamellar crystals increased after relaxation of the molecular chains with a planar zigzag conformation (β-form) between the lamellar crystals (α-form). Reversible elastic properties were regenerated by a planar zigzag conformation between the lamellar crystals, the extension of molecular chains in lamellar crystals by the rotation of molecular conformation, and changes in the degree of orientation of the lamellar crystals.

Non-fullerene acceptors based on multiple non-covalent interactions for low cost and air stable organic solar cells

Significant progresses have been made on organic solar cells (OSCs) in last few years, but the industrialization of OSCs is still hindered by high cost and poor device stability. Recently, the most successful OSCs are usually based on fused-ring small molecule non-fullerene acceptors (SM-NFAs) which often involve multiple complex synthetic steps and result in low overall yields and high cost. Herein, two easily accessible non-fused NFAs based on BT , CPDT and IC with different halogen atoms named BT-F and BT-Cl were designed and synthesized. Non-covalent interactions or conformation locks between BT and adjacent CPDT units provided planar conformations, which is beneficial for molecular packing and charge transport. When blended with low cost polymer donor PTQ-10 , optimal devices based on BT-F provided a PCE of 8.26%. A higher PCE of 8.65% was obtained from BT-Cl -based devices. Low voltage loss of 0.57 and 0.59 V were observed for BT-F - and BT-Cl -based devices. It is noteworthy that devices based on PTQ-10 : BT-F and PTQ-10 : BT-Cl exhibited excellent stabilities when stored in ambient atmosphere for 10 days without encapsulation. This work demonstrates an example of pursuing low cost OSCs with excellent air stability. • Two non-fused non-fullerene acceptors named BT-F and BT-Cl were reported. • When blend with PTQ-10, BT-F and BT-Cl show PCEs of 8.26% and 8.65%, respectively. • The devices exhibit excellent air stabilities without encapsulation.

Red to Near-Infrared Mechanochromism from Metal-free Polycrystals: Noncovalent Conformational Locks Facilitating Wide-Range Redshift.

Piezochromic organic materials that present a large difference in fluorescence wavelength in the near-infrared region have important potential applications; however, few such metal-free luminophores have been reported. In this study, we design and prepare π-conjugated electron acceptors whose planar conformation can be locked by the noncovalent interactions. The planar fused-ring geometry can narrow the optical band gap, enhance the molecular stability and rigidity, as well as increase the radiative rate. As expected, the polymorphs Re-phase and Ni-phase emit the high-brightness fluorescence with wavelength maxima (λem,max ) at 615 and 727 nm, respectively. Upon full grinding, the λem,max of Re-phase is bathochromically shifted to 775 nm. The ground powder of Re-phase becomes metastable as a consequence of noncovalent conformational locking and that the red to near-infrared (large colour difference) mechanochromism arises from the high degree of conformational coplanarity. This strategy is both conceptually and synthetically simple and offers a promising approach to the development of organic piezochromic materials with wide-range redshift and excellent penetrability.

Red to Near‐Infrared Mechanochromism from Metal‐free Polycrystals: Noncovalent Conformational Locks Facilitating Wide‐Range Redshift

AbstractPiezochromic organic materials that present a large difference in fluorescence wavelength in the near‐infrared region have important potential applications; however, few such metal‐free luminophores have been reported. In this study, we design and prepare π‐conjugated electron acceptors whose planar conformation can be locked by the noncovalent interactions. The planar fused‐ring geometry can narrow the optical band gap, enhance the molecular stability and rigidity, as well as increase the radiative rate. As expected, the polymorphs Re‐phase and Ni‐phase emit the high‐brightness fluorescence with wavelength maxima (λem,max) at 615 and 727 nm, respectively. Upon full grinding, the λem,max of Re‐phase is bathochromically shifted to 775 nm. The ground powder of Re‐phase becomes metastable as a consequence of noncovalent conformational locking and that the red to near‐infrared (large colour difference) mechanochromism arises from the high degree of conformational coplanarity. This strategy is both conceptually and synthetically simple and offers a promising approach to the development of organic piezochromic materials with wide‐range redshift and excellent penetrability.

When Does Fusing Two Rings Not Yield a Larger Ring? The Curious Case of BOPHY.

Structural and electronic features of ground and excited states of the bis(difluoroboron)-1,2-bis-(pyrrol-2-yl)methylene-hydrazine (BOPHY) fluorophore, a seemingly extended version of the popular 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) fluorophore, are presented. Geometries of S0 and S1 electronic states are highly puckered, as confirmed by a combination of density functional theory (DFT), time-dependent (TD)-DFT, CASSCF-PT2, EOM-CCSD calculations and density functional theory-based molecular dynamics (DFT-MD). Packing effects are responsible for planarization in the solid state. Without the network of a solid matrix, planar conformation of BOPHY is an easily accessible transition state of inversion between two puckered conformations and hence solvated BOPHY is suggested to sample the conformational space between the two puckered geometries. The peculiar features of puckering as well as inversion via a planar TS are unaltered with a large range of lateral substitutions. Concentration-dependent electronic absorbance measurements were carried, which showed that the transformation of the low activation energy between the puckered and planar conformations is responsible for the broadening of the absorption spectrum. BOPHY, a four-ring system, is not an electronic extension of the three-ring BODIPY system since the excitation characteristics suggest BOPHY to behave as two electronically unlinked fragments despite the fact that the two subunits are covalently bonded.

Facilitated phase transformation of PVDF in its composite with an ionic liquid

The phase transition of poly(vinylidene fluoride) (PVDF) from α-to γ′-phase is hardly accessible, especially for the low-temperature crystallized α-phase, owing to the diminished thermal energy available for transformation. In this study, the phase transition ability of α-PVDF is greatly improved in its composites with a typical imidazole ionic liquid, 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6]). The enhanced phase transition is achieved by two thermal steps, including the crystallization of α-phase and subsequent annealing at a higher temperature. The transformed lamellar morphology is dependent on the crystallization temperature of α-phase, while the phase transition efficiency mainly rests with the annealing temperature. The phase transition is always accompanied by the thermal degradation with elimination of HF, which is significantly accelerated by [BMIM][PF6]. The introduction of molecular defects and carbon-carbon double bonds probably increase the fraction of planar chain conformation, therefore, enhancing the phase transition efficiency.

Molecular design revitalizes the low-cost PTV-polymer for highly efficient organic solar cells.

Developing photovoltaic materials with simple chemical structures and easy synthesis still remains a major challenge in the industrialization process of organic solar cells (OSCs). Herein, an ester substituted poly(thiophene vinylene) derivative, PTVT-T, was designed and synthesized in very few steps by adopting commercially available raw materials. The ester groups on the thiophene units enable PTVT-T to have a planar and stable conformation. Moreover, PTVT-T presents a wide absorption band and strong aggregation effect in solution, which are the key characteristics needed to realize high performance in non-fullerene-acceptor (NFA)-based OSCs. We then prepared OSCs by blending PTVT-T with three representative fullerene- and NF-based acceptors, PC71BM, IT-4F and BTP-eC9. It was found that PTVT-T can work well with all the acceptors, showing great potential to match new emerging NFAs. Particularly, a remarkable power conversion efficiency of 16.20% is achieved in a PTVT-T:BTP-eC9-based device, which is the highest value among the counterparts based on PTV derivatives. This work demonstrates that PTVT-T shows great potential for the future commercialization of OSCs.

The CH···HC interaction in biphenyl is a delocalized, molecular-wide and entirely non-classical interaction: Results from FALDI analysis.

In this study we aim to determine the origin of the electron density describing a CH···HC interaction in planar and twisted conformers of biphenyl. In order to achieve this, the fragment, atomic, localized, delocalized, intra- and inter-atomic (FALDI) decomposition scheme was utilized to decompose the density in the inter-nuclear region between the ortho-hydrogens in both conformers. Importantly, the structural integrity, hence also topological properties, were fully preserved as no 'artificial' partitioning of molecules was implemented. FALDI-based qualitative and quantitative analysis revealed that the majority of electron density arises from two, non-classical and non-local effects: strong overlap of ortho CH σ-bonds, and long-range electron delocalization between the phenyl rings and ortho carbons and hydrogens. These effects resulted in a delocalized electron channel, that is, a density bridge or a bond path in a QTAIM terminology, linking the H-atoms in the planar conformer. The same effects and phenomena are present in both conformers of biphenyl. We show that the CH···HC interaction is a molecular-wide event due to large and long-range electron delocalization, and caution against approaches that investigate CH···HC interactions without fully taking into account the remainder of the molecule.

Effect of Nanopore Geometry in the Conformation and Vibrational Dynamics of a Highly Confined Molecular Glass.

The effect of nanoporous confinement on the glass transition temperature (Tg) strongly depends on the type of porous media. Here, we study the molecular origins of this effect in a molecular glass, N,N'-bis(3-methylphenyl)-N,N'-diphenylbenzidine (TPD), highly confined in concave and convex geometries. When confined in controlled pore glass (CPG) with convex pores, TPD's vibrational spectra remained unchanged and two Tg's were observed, consistent with previous studies. In contrast, when confined in silica nanoparticle packings with concave pores, the vibrational peaks were shifted due to more planar conformations and Tg increased, as the pore size was decreased. The strong Tg increases in concave pores indicate significantly slower relaxation dynamics compared to CPG. Given TPD's weak interaction with silica, these effects are entropic in nature and are due to conformational changes at molecular level. The results highlight the role of intramolecular degrees of freedom in the glass transition, which have not been extensively explored.

Benzo/Naphthodifuranone-Based Polymers: Effect of Perpendicular-Extended Main Chain π-Conjugation on Organic Field-Effect Transistor Performances.

For polymer semiconductors, the backbone structure plays an essential role in determining their physicochemical properties and charge transport behaviors. In this work, two donor-acceptor-type polymers (P-BDF and P-NDF) based on benzodifuranone (BDF) and naphthodifunarone (NDF) as electron-deficient moieties and indaceno-dithiophene as electron-rich groups are designed, synthesized and, for the first time, applied in organic field-effect transistor. P-BDF and P-NDF differ from their backbone structures while P-BDF has a more planar backbone conformation due to its smaller conjugated core size and P-NDF features a perpendicular-extended main chain structure. As a result, P-BDF polymer exhibits bathochromic optical absorption, deeper molecular orbital energy levels, and more importantly, closer π-stacking and stronger aggregation in the solid state and thus affords a more promising hole mobility of up to 0.85 cm2 V-1 s-1 in OFET devices, while that of the P-NDF-based devices is only 0.55 cm2 V-1 s-1 . The results suggest the great potential of BDF/NDF-type chromophores in constructing novel organic semiconductors and also indicate that the main chain coplanarity of polymer semiconductors is more essential than the sole extension of π-conjugations (especially at the perpendicular direction of polymer main chains) for the design of high-performance OFET materials.

Difluoroterthiophene as promising block to build highly planar conjugated polymer for polymer photovoltaic cells

Developing highly planar semiconducting polymer is essential for achieving high mobility and improving the photovoltaic performance of bulk-heterojunction polymer solar cells. In this contribution, two novel low-bandgap donor-acceptor copolymers, P1-3T and P2-3T2F, consisting of electron-accepting benzothiadiazole acceptor segment and electron-donating terthiophene donor segment with and without fluorine atoms were designed and synthesized. The density functional theory calculations and ultraviolet–visible absorption studies demonstrate that the fluorinated P2-3T2F polymer has more planar backbone conformation, deeper HOMO level, broader absorption spectrum with a vibronic shoulder peak, and higher absorption coefficient compared with the non-fluorinated analogue polymer, P1-3T. Furthermore, P2-3T2F exhibits good crystallinity and high hole mobility, presumably due to the well-ordered lamellar packing and the π-π stacking interaction between the backbones of the conjugated polymers. The optimized polymer solar cell based on P2-3T2F:PC61BM exhibits a short-circuit current density (Jsc) of 12.77 mA cm−2, a fill factor (FF) of 68.99%, an open-circuit voltage (Voc) of 0.80 V, and a maximum power conversion efficiency (PCE) of 7.14%, which is approximately 46% higher than that of the P1-3T:PC61BM device. The enhanced PCE is primarily due to increased light-harvesting ability and interconnected morphology with finely dispersed polymer-rich and PC61BM-rich domains, which improves the efficiency of exciton dissociation and rises the mobility of charge carriers, thus boosting the short-circuit current density and the FF value. Moreover, the relatively deep HOMO of P2-3T2F effectively increases the Voc.

Effect of solvent on the photophysical properties of isoxazole derivative of curcumin: A combined spectroscopic and theoretical study

The present work aims to decipher the photophysics of a β-diketo modified curcumin analog named isoxazole derivative of curcumin (IOC). IOC itself happens to be a potential drug molecule possessing numerous biological applications such as; anti-cancer, anti-malarial, anti-Alzheimer’s, anti-Parkinson’s etc. Herein, the photophysical properties of IOC have been explored in various sets of solvents. In order to investigate, steady state and time resolved spectroscopy have been utilized as a tool. To elucidate the experimental observations at molecular level, electronic structure calculations with density functional theory (DFT) as well as classical molecular dynamics (MD) simulations in explicit solvents have been deployed. The DFT has established that the most stable ground state electronic structure of the IOC molecule is the all trans- planar conformation where the conjugated pi-electrons are delocalized over the entire molecule. The MD simulations have provided an insight into the specific and non-specific interactions with the solvent molecules. Steady state spectroscopic techniques have shown that both the absorption and emission maxima experienced a traditional red shift upon increase in the solvent polarity. The absorption maxima for IOC got red shifted from 332 nm in hexane to 344 nm in DMSO. However, the red shift in the emission maxima is more pronounced than that of absorption maxima starting from 356 nm in hexane to 431 nm in water. The value of molar extinction coefficient has also been determined for IOC in different solvents from the concentration dependent absorption spectra. The time correlated single photon counting (TCSPC) data has revealed that the excited state of IOC molecule could relax via three probable pathways. Also, the overall process of decay of the excited state is comparatively slower in case of non-polar solvents. On the other hand, the fluorescence lifetime has been observed to be unusually low in case of dimethyl sulfoxide (DMSO) as compared to its other fellow polar aprotic solvents.

Crystal structure and fluorescence study of (μ-N-[(3,5-dimethyl-1H-pyrrol-2-yl)methyl-idene]-N-{4-[(3,5-dimethyl-1H-pyrrol-2-yl)methyl-idene-aza-nium-yl]phen-yl}aza-nium)bis-[di-fluorido-boron(IV)

The title mol-ecule, C20H20B2F4N4, assumes a planar conformation with all atoms apart from the F atoms lying on the symmetry plane. Each boron atom is four-coordinated by two fluorine atoms, a pyrrole N atom and an imine N atom. Both imine CH=N groups adopt a trans conformation. In the crystal, the mol-ecules self-assemble into a pillar structure through C-H⋯F hydrogen bonds and π-π inter-actions. The UV-vis spectrum and fluorescence spectra of the title compound are also reported.

Molecular engineering enabling reversible transformation between helical and planar conformations by cyclization of alkynes.

Molecular engineering enabling reversible transformation between helical and planar conformations is described herein. Starting from easily available 2-(pyridin-2-yl)anilines and alkynes, a one-pot strategy is set up for the synthesis of aza[4]helicenes via two successive rhodium-catalyzed C–H activation/cyclizations. Helical pyrrolophenanthridiziniums can be transformed into planar conformations through the cleavage of acidic pyrrole N–H, leading to turn-off fluorescence. NMR spectra, single crystal X-ray diffraction and DFT calculations demonstrate that the formation of an intramolecular C–H⋯N hydrogen bond is beneficial to stabilize the pyrrole nitrogen anion of the planar molecule and provide increased planarity. The reversible conformation transformations can be finely adjusted by the electron-donating and -withdrawing groups on the π+-fused pyrrole skeleton in the physiological pH range, thus affording an opportunity for pH-controlled intracellular selective fluorescence imaging. Pyrrolophenanthridiziniums show turn-on fluorescence in lysosomes owing to the acidic environment of lysosomes and turn-off fluorescence out of lysosomes, indicating the occurrence of the deprotonation reaction outside lysosomes and the corresponding transformation from helical to planar conformations.

Space conjugation induced white light and room-temperature phosphorescence from simple organic small molecules: single-component WLED driven by both UV and blue chips

Simple molecule TIM with planar conformation and rich heteroatoms exhibits white emission and yellow phosphorescence for space conjugation. TIM powder can be employed as a single-component material to fabricate WLEDs driven by both UV and blue chips.

Highly broadband NLO response of acceptor–donor–acceptor materials with a planar conformation

The third-order NLO properties of A–D–A molecules originally derived from organic photovoltaic (OPV) devices are studied. The results show that NLO performance of planar molecule (O-IDTBR) is better than that of twisted molecule (IDFBR) in solution or film state.