Zigzag Backbone Research Articles

Azobenzene-Based Main-Chain Liquid Crystalline Polymers Bearing Periodically Installed Alkyl, PEG, or Fluoroalkyl Segments and Photoisomerization Studies

ABSTRACT In the present study, liquid crystalline polymers (LCPs) were prepared by melt-transesterification of azobenzene-bearing diols and diethyl malonate (DEM) derivatized monomers. The effect of the nature and length of the installed pendant segments on the mesomorphic properties of the prepared LCPs was investigated by differential scanning calorimetry (DSC), X-ray diffraction (XRD), and polarized optical microscopy (POM) studies. The formation of layered morphology was inferred from X-ray scattering analysis arising from the colocation of rigid azobenzene moieties in one layer and the flexible pendant segments in alternate layers due to the zigzag folding of the polymer backbone. The linear variation of the interlamellar spacing with the number of carbon atoms in the pendant alkyl segments corroborates the proposed zigzag backbone folding in the polymers. The rate constant values obtained from the photoisomerization studies of the isomeric polymers and model compound, which are in the same ballpark, reveal that the photoisomerization process of such polymers is not affected by the position or size of the azobenzene unit.

Approaching disorder-tolerant semiconducting polymers

Doping has been widely used to control the charge carrier concentration in organic semiconductors. However, in conjugated polymers, n-doping is often limited by the tradeoff between doping efficiency and charge carrier mobilities, since dopants often randomly distribute within polymers, leading to significant structural and energetic disorder. Here, we screen a large number of polymer building block combinations and explore the possibility of designing n-type conjugated polymers with good tolerance to dopant-induced disorder. We show that a carefully designed conjugated polymer with a single dominant planar backbone conformation, high torsional barrier at each dihedral angle, and zigzag backbone curvature is highly dopable and can tolerate dopant-induced disorder. With these features, the designed diketopyrrolopyrrole (DPP)-based polymer can be efficiently n-doped and exhibit high n-type electrical conductivities over 120 S cm−1, much higher than the reference polymers with similar chemical structures. This work provides a polymer design concept for highly dopable and highly conductive polymeric semiconductors.

Influence of Bridging Groups on the Photovoltaic Properties of Wide-Bandgap Poly(BDTT- alt-BDD)s.

To further advance polymer solar cells requires the fast evolution of π-conjugated materials as well as a better understanding of their structure-property relationships. Herein, we present three copolymers (PT1, PT2, PT3) made through tuning π-bridges (without any group, thiophene, and 3-hexylthieno[3,2- b]thiophene) between electron-rich (D: BDTT) and -deficient (A: BDD) units. The comparative studies reveal the unique correlation that the tune of π-bridge on the polymeric backbone governs the solid stacking and photovoltaic properties of resultant poly(BDTT- alt-BDD)s, which provide an effective way to deliver new and efficient polymer with feasible processability. That is, polymers with either twist zigzag backbone (PT1) or with linear coplanar backbone (PT2) result in inferior photovoltaic performance upon simple solution casting. Among them, PT3 with extended zigzag backbone and planar segments exhibits suitable processability and retains good efficiency in nonfullerene solar cells through a single-solvent cast without involving tedious treatments. This work illustrates that the tuning of the D-π-A polymer backbone facilitates efficient materials with feasible processability, promising for scale-up fabrication.

A B–Z junction induced by an A … A mismatch in GAC repeats in the gene for cartilage oligomeric matrix protein promotes binding with the hZαADAR1 protein

GAC repeat expansion from five to seven in the exonic region of the gene for cartilage oligomeric matrix protein (COMP) leads to pseudoachondroplasia, a skeletal abnormality. However, the molecular mechanism by which GAC expansions in the COMP gene lead to skeletal dysplasias is poorly understood. Here we used molecular dynamics simulations, which indicate that an A … A mismatch in a d(GAC)6·d(GAC)6 duplex induces negative supercoiling, leading to a local B-to-Z DNA transition. This transition facilitates the binding of d(GAC)7·d(GAC)7 with the Zα-binding domain of human adenosine deaminase acting on RNA 1 (ADAR1, hZαADAR1), as confirmed by CD, NMR, and microscale thermophoresis studies. The CD results indicated that hZαADAR1 recognizes the zigzag backbone of d(GAC)7·d(GAC)7 at the B-Z junction and subsequently converts it into Z-DNA via the so-called passive mechanism. Molecular dynamics simulations carried out for the modeled hZαADAR1-d(GAC)6d(GAC)6 complex confirmed the retention of previously reported important interactions between the two molecules. These findings suggest that hZαADAR1 binding with the GAC hairpin stem in COMP can lead to a non-genetic, RNA editing-mediated substitution in COMP that may then play a crucial role in the development of pseudoachondroplasia.

Synthesis and characterization of main‐chain, second‐order, nonlinear optical polyurethanes with isolation moieties and zigzag structures

ABSTRACTIn this study, two main‐chain second‐order nonlinear optical (NLO) polyurethanes were successfully prepared with indole‐based chromophores. The introduced phenyl isolation group and the continuous zigzag polymer backbone were found to be helpful for effectively decreasing the intermolecular dipole–dipole interactions and enhancing the NLO properties of the resulting polymers. The studied polymers exhibited good optical transparency, high thermal stability, and excellent NLO effects; this indicated that the nonlinearity–stability trade‐off and nonlinearity–transparency trade‐off could be alleviated by this newly designed polymer system. Poly{4‐anilinocarbonyl[N‐ethoxyl‐5‐phenyl‐3‐azo(2′‐oxyethylene‐4′‐nitrobenzene)indole]carbonylimino} with a zigzag backbone showed a large second harmonic generation coefficient (d33) value of 88.4 pm/V. However, poly{5‐naphthyliminocarbonyl[N‐ethoxyl‐5‐phenyl‐3‐azo(2′‐oxyethylene‐4′‐nitrobenzene)indole]carbonylimino} (PUAZN) with a continuous zigzag structure exhibited a higher d33 value of 116.2 pm/V, which was attributed to the unique rigid and zigzag linkage of 1,5‐naphthalene as the isolation spacer. The enhanced NLO efficiency and relatively longer term temporal stability made PUAZN as a promising candidate for practical applications in photonic devices. © 2015 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2016, 133, 42974.

Is Single-4-Ring the Most Basic but Elusive Secondary Building Unit That Transforms to Larger Structures in Zinc Phosphate Chemistry?

Haloaryl phosphates (X-dippH2, X = Cl, Br, I) react with zinc acetate in the presence of collidine or 2-aminopyridine (2-apy) to yield zinc phosphate clusters [Zn(X-dipp)(collidine)]4 (X = Cl (1), Br (2), I (3)) and [Zn(X-dipp)(2-apy)]4·2MeOH (X = Cl (4), Br (5), I (6)), respectively. Single-crystal X-ray diffraction studies reveal that collidine and 2-apy capped zinc phosphates 1-6 exist as discrete tetrameric zinc phosphate molecules, exhibiting a cubane-shaped D4R core. In contrast, when the same reaction has been carried out in the presence of 4-cyanopyridine (4-CNpy), polymeric zinc phosphates {[Zn4(X-dipp)4(4-CNpy)2(MeOH)2]·2H2O}n (X = Cl (7), Br (8), I (9)) have been isolated. Compounds 7-9 are square-wave-shaped, one-dimensional polymers composed of fused S4R repeating units. The common structural motif found both in D4R cubanes 1-6 and polymers 7-9 is the S4R building block, which presumably undergoes further fusion because of the coordinative unsaturation at zinc and the simultaneous presence of free P═O. The closed shell cubanes 1-6 are obviously formed by a face-to-face dimerization involving two S4R units in which the two P═O groups are in cis-configuration. On the other hand, the one-dimensional (1-D) square-wave polymers 7-9 are formed from a face-to-face association of S4R building units in which the two P═O groups are in a trans-configuration. In order to stabilize these elusive S4R zinc phosphates, the reaction between Cl-dippH2 and zinc acetate was carried out in the presence of excess imidazole as an ancillary ligand (1:1:4), although only an imidazole decorated cubane cluster [Zn(Cl-dipp)(imz)]4.2MeOH (10) was isolated. The chelating N,N'-donor 1,10-phenanthroline ligand was used to eventually isolate cyclic S4R phosphate [Zn(μ2-Cl-dipp)(1,10-phen)(OH2)]2·MeOH·H2O (11). The change of Zn(2+) source to zinc nitrate and the phosphate source to 2,6-dimethylphenyl phosphate (dmppH2) led to the isolation of another polymeric phosphate [Zn(dmpp)(MeOH)]n (12), with a zigzag backbone, formed through an edge-to-edge to polymerization of S4R building units with P═O groups in trans-configuration. The isolation of four different structural types of zinc phosphates A-D in the present study can be rationalized in terms of fusion of S4R rings in a variety of ways to either produce discrete clusters or 1-D polymers.

Crystal structure of 2,2,3,3-tetra-methyl-1,1,1,4,4,4-hexa-phenyl-tetra-germane.

The mol­ecule of the title compound, C40H42Ge4, lies with its central Ge—Ge bond on an inversion centre giving rise to a zigzag backbone of four tetra­hedrally coordinated Ge atoms. The symmetrically independent Ge—Ge bonds are slightly shorter than in other organo­tetra­germanes whereas the Ge—CPh (Ph = phen­yl) and Ge—CMe (Me = meth­yl) distances have their usual values. In the crystal, (010) layers of Ph6Me4Ge4 mol­ecules with a parallel orientation of the Ge4 backbone exist, held together by van der Waals forces only. Main bond lengths in organo-substituted oligogermanes are compared.

Conjugated Polymer Assemblies on Carbon Nanotubes

The assembling behavior of four thiophene-containing conjugated polymers, regioregular poly(3-hexythiophene) (rr-P3HT), poly(3,3-didodecylquaterthiophene) (PQT-12), poly(2,5-bis(3- tetradecylthiophen-2-yl)thieno[3,2-b]thiophene) (PBTTT-14), and poly(2,5-bis(3-tetradecylthiophen-2-yl)thiophen-2-yl)thiophen-2-ylthiazolo[5,4-d]thiazole) (PTzQT-14), on carbon nanotubes was investigated through microscopic studies of nanowire formation and theoretical simulation. It is found that polymer backbone rigidity and shape influence the attachment mode on carbon nanotubes. rr-P3HT and PQT-12 have a zigzag backbone structure that allows a thermodynamically stable coaxial attachment on CNTs, providing an ordered growth front for the nanowire formation. In contrast, fused rings in PTzQT-14 and PBTTT-14 create a stair-step like backbone structure that causes a kinetically controlled wrapping conformation on CNTs, generating a twisted growth front that hinders the nanowire formation. In addition, the rigidity of polymer backbone influences the wrapping mode. Polymers with more flexible backbones (i.e., PBTTT-14) would take a dense irregular wrapping mode on CNTs. The CNT diameter plays an important role in the nanowire formation when CPs attach to the CNT in the wrapping mode. Larger nanotubes with smaller surface curvature provides a less twisted polymer growth front, allowing the formation of CPNWs.

Hydrogen-bonding network ofN,N′-bis[2-(tert-butyldimethylsiloxy)ethyl]ethylenediammonium dichloride

The title salt, C18H46N2O2Si2(2+)·2Cl(-), has been synthesized by reaction of N,N'-bis(2-hydroxyethyl)ethylenediamine with tert-butyldimethylsilyl chloride. The zigzag backbone dication is located across an inversion centre and the two chloride anions are related by inversion symmetry. The ionic components form a supramolecular two-dimensional network via N-H···Cl hydrogen bonding, which is responsible for the high melting point compared with the oily compound N,N'-bis[2-(tert-butyldimethylsiloxy)ethyl]ethylenediamine.

A tetranuclear cobalt(ii) chain with slow magnetization relaxation

A solvothermally derived tetranuclear cobalt(II) complex, [Co(4)(phen)(4)Cl(8)] (phen = phenanthroline), featuring a zig-zag backbone of {Co(μ(2)-Cl)(2)Co} planes, exhibits ferromagnetic exchange and slow relaxation of the magnetization and represents the first Co SMM with a linear core structure.

ALEXANDER RICH WINS WELCH AWARD

FOR HIS PIONEERING WORK on nucleic acids, Alexander Rich, a professor of biophysics at MIT, has won the 2008 Welch Award in Chemistry. The $300,000 award is given annually by Houston’s Welch Foundation to foster and encourage basic chemical research that benefits humankind. A student of Linus Pauling’s and a contemporary of James Watson and Francis Crick’s, Rich has devoted his entire career to studying DNA and RNA. In 1979, he and his colleagues discovered left-handed DNA, which they named Z-DNA for its zigzag backbone. Since then, Rich’s research has focused on Z-DNA’s importance in biological systems. In addition, Rich discovered and solved the three-dimensional structure of the RNA double helix. He was the first scientist to carry out DNA-RNA hybridization and to discover DNA’s presence in organelles. He also discovered polyribosomes, which are clusters of ribosomes attached to messenger RNA, and determined the three-dimensional structure of transfer RNA. Rich is known for his enthusiasm ...

Boundary lubrication additives for aluminium: A journey from nano to macrotribology

The tribology of two potential additive molecules for aluminium has been studied in the self assembled monolayer state at low loads (10 −9–10 −2 N) and in dispersion state in n-hexadecane at high load (60 N). The two additive molecules are 1H, 1H, 2H, 2H-perfluorooctyltrichlorosilane (FOTS), which has a rigid rod-like helical structure and octadecyltrichlorosilane (OTS), which has a zigzag backbone configuration. The adhesion, friction and wear performance have been investigated. Molecular conformational order and stiffness were found to play major roles in frictional dissipation and wear resistance, recorded in a nanotribometer and a pin-on-disc machine, while for very low load measurements (LFM), adhesion was found to have a significant role on friction along with molecular entropy.

New insights into DNA triplexes: residual twist and radial difference as measures of base triplet non-isomorphism and their implication to sequence-dependent non-uniform DNA triplex.

DNA triplexes are formed by both isomorphic (structurally alike) and non-isomorphic (structurally dissimilar) base triplets. It is espoused here that (i) the base triplet non-isomorphism may be articulated in structural terms by a residual twist (Δt°), the angle formed by line joining the C1′…C1′ atoms of the adjacent Hoogsteen or reverse Hoogsteen (RH) base pairs and the difference in base triplet radius (Δr Å), and (ii) their influence on DNA triplex is largely mechanistic, leading to the prediction of a high (t + Δt)° and low (t − Δt)° twist at the successive steps of Hoogsteen or RH duplex of a parallel or antiparallel triplex. Efficacy of this concept is corroborated by molecular dynamics (MD) simulation of an antiparallel DNA triplex comprising alternating non-isomorphic G*GC and T*AT triplets. Conformational changes necessitated by base triplet non-isomorphism are found to induce an alternating (i) high anti and anti glycosyl and (ii) BII and an unusual BIII conformation resulting in a zigzag backbone for the RH strand. Thus, base triplet non-isomorphism causes DNA triplexes into exhibiting sequence-dependent non-uniform conformation. Such structural variations may be relevant in deciphering the specificity of interaction with DNA triplex binding proteins. Seemingly then, residual twist (Δt°) and radial difference (Δr Å) suffice as indices to define and monitor the effect of base triplet non-isomorphism in nucleic acid triplexes.

A poxvirus protein forms a complex with left-handed Z-DNA: crystal structure of a Yatapoxvirus Zalpha bound to DNA.

A conserved feature of poxviruses is a protein, well characterized as E3L in vaccinia virus, that confers IFN resistance on the virus. This protein comprises two domains, an N-terminal Z-DNA-binding protein domain (Zalpha) and a C-terminal double-stranded RNA-binding domain. Both are required for pathogenicity of vaccinia virus in mice infected by intracranial injection. Here, we describe the crystal structure of the Zalpha domain from the E3L-like protein of Yaba-like disease virus, a Yatapoxvirus, in a complex with Z-DNA, solved at a 2.0-A resolution. The DNA contacting surface of Yaba-like disease virus Zalpha(E3L) closely resembles that of other structurally defined members of the Zalpha family, although some variability exists in the beta-hairpin region. In contrast to the Z-DNA-contacting surface, the nonbinding surface of members of the Zalpha family are unrelated; this surface may effect protein-specific interactions. The presence of the conserved and tailored Z-DNA-binding surface, which interacts specifically with the zigzag backbone and syn base diagnostic of the Z-form, reinforces the importance to poxvirus infection of the ability of this protein to recognize the Z-conformation.

Structure of solid monolayers and multilayers ofn-hexane on graphite

We present all-atom molecular dynamics simulations ofn-hexane on the basal plane of graphite at monolayer and multilayer coverages. In keeping with experimental data, we find the presence of ordered adsorbed layers both at single monolayer coverage and when the adsorbed layer coexists with excess liquid adsorbate. Using a simulation method that does not impose any particular periodicity on the adsorbed layer, we quantitatively compare our results to the results of neutron diffraction experiments and find a structural transition from a uniaxially incommensurate lattice to a fully commensurate structure on increasing the coverage from a monolayer to a multilayer. The zig-zag backbone planes of all the alkane molecules lie parallel to the graphite surface at the multilayer coverage, while a few molecules are observed to attain the perpendicular orientation at monolayer coverage.

An atomistic simulation study of a solid monolayer and trilayer of n-hexane on graphite

We present all-atom molecular dynamics simulations of n-hexane on the basal plane of graphite at monolayer and trilayer coverages. In keeping with experimental data, we find the presence of ordered adsorbed layers at both coverages. Using a simulation method that does not impose any particular periodicity on the adsorbed layer, we quantitatively compare our results to the results of neutron diffraction experiments and find a structural transition from a uniaxially incommensurate lattice to a fully commensurate structure on increasing the coverage from a monolayer to a trilayer. The zig–zag backbone planes of all the alkane molecules lie parallel to the graphite surface at the trilayer coverage, while a few molecules are observed to attain the perpendicular orientation at monolayer coverage.

Conformational Analysis of meso-2,3,4,5-Tetramethylhexane and Some of Its Derivatives

Compounds 12−15, meso-type 2,3,4,5,6,7-hexasubstituted octane derivatives, have been synthesized using solely substrate-based asymmetric induction. Thanks to the specific relative configurations at the six stereogenic centres, these compounds have a high tendency to populate the conformation with a fully extended zig-zag backbone chain.

Conformational Analysis ofmeso-2,3,4,5-Tetramethylhexane and Some of Its Derivatives

Compounds 12−15, meso-type 2,3,4,5,6,7-hexasubstituted octane derivatives, have been synthesized using solely substrate-based asymmetric induction. Thanks to the specific relative configurations at the six stereogenic centres, these compounds have a high tendency to populate the conformation with a fully extended zig-zag backbone chain.

Solitons in crystalline polyethylene: A chain surrounded by immovable neighbors

A numerical solution to the problem of existence and stability of topological solitons in a polyethylene chain surrounded by immovable neighboring chains is obtained. In the framework of a realistic model that takes into account deformations of valence bonds, valence and torsional angles, as well as intermolecular interactions, three types of solitons describing local topological defects in the crystal are found. They correspond, respectively, to (i) stretching or compression of the zigzag backbone by one lattice spacing, (ii) stretching or compression over half-lattice spacing together with twisting by $180\ifmmode^\circ\else\textdegree\fi{},$ and (iii) pure twisting by $360\ifmmode^\circ\else\textdegree\fi{}.$ The existence of such solitons is caused by specific topology of the polyethylene crystal. For each of these solitons the velocity spectrum is found in the subsonic region. Molecular-dynamics modeling leads to conclusion about their stability in the whole interval of admissible velocities. The influence of temperature is also taken into account. It is shown that thermal vibrations can result only in the formation of the second type of solitons. These solitons are created as kink-antikink pairs that can move along the chain as Brownian particles. The abrupt increase of the soliton density is shown to occur near the crystal melting point.

Neutron structure analysis of poly(vinyl alcohol)

Different crystal structure models have been proposed for atactic poly(vinyl alcohol) by two groups: Bunn and Sakurada et al. The models differ principally in the azimuthal angle of the planar zigzag backbone and the hydrogen bonding network. In the present study, reexamination of the crystal structure analysis was carried out by using both the X-ray and neutron diffraction methods. The crystal structure model proposed by Bunn is found to be superior. The (Fo − Fc) synthesis was made for the neutron data (100 K), in which the hydrogen atoms to be associated with the hydrogen bonds are not incorporated into Fc calculation. On the map, three peaks were found, which may be attributed to the hydrogen atoms to be associated with the intramolecular hydrogen bonds between OH groups in an isotactic sequence and the two kinds of intermolecular hydrogen bonds. © 1997 John Wiley & Sons, Inc.