Open-chain Oligomers Research Articles

Structural Expansion of Catalytic RNA Nanostructures through Oligomerization of a Cyclic Trimer of Engineered Ribozymes.

The multimolecular assembly of three-dimensionally structured proteins forms their quaternary structures, some of which have high geometric symmetry. The size and complexity of protein quaternary structures often increase in a hierarchical manner, with simpler, smaller structures serving as units for larger quaternary structures. In this study, we exploited oligomerization of a ribozyme cyclic trimer to achieve larger ribozyme-based RNA assembly. By installing kissing loop (KL) interacting units to one-, two-, or three-unit RNA molecules in the ribozyme trimer, we constructed dimers, open-chain oligomers, and branched oligomers of ribozyme trimer units. One type of open-chain oligomer preferentially formed a closed tetramer containing 12 component RNAs to provide 12 ribozyme units. We also observed large assembly of ribozyme trimers, which reached 1000 nm in size.

Molecular simulations of liquid aliphatic carboxylic acids (C1-C6) using the 3D-RISM-KH molecular solvation theory

The liquid structures of short straight chain aliphatic carboxylic acids (C1-C6) and halogenated acetic acids (trifluoro and trichloro) are analyzed with molecular dynamics simulations, three-dimensional reference interaction site model, and density functional theory calculations. The neat acids are found to exist in multimeric ordered form consisting of both open chain and cyclic oligomers. Introduction of water breaks the hydrogen bonding networks between adjacent acetic acid molecules by inserting water as a bridging molecule. The electronic structure calculations confirm the formation of chain and ring type structures in the liquid state.

Reactions of permethyltitanocene tucked-in derivatives with carbon dioxide.

Both single tucked-in permethyltitanocene 1 and double tucked-in permethyltitanocene 2 react with excess CO2 by insertion into their Ti-CH2 bonds. The former one precipitates instantly a yellow carboxylate-tethered oligomer [3]n which is insoluble in aprotic solvents and in a vacuum it sublimes as a monomer without decomposition. Computations for n ≤ 4 optimised the structure of the monomer [3] and showed that open chain oligomers bound by dative O → Ti bonds were not sterically hindered. The latter bond dissociates when [3]n is oxidized by chlorination with CDCl3 or CD2Cl2 to give Ti(IV) chloride 4 or upon metathesis of [3]n with Me3SiCl yielding Ti(III) chloride 5. Oxidative addition of MeCN affords a C-C coupled dinuclear titanocene diimine 6. Compound [3]n also reacts with 1 to give the tethered carbodiolate 8 or with [Cp*2TiH] (where Cp* = η5-C5Me5) to give the half-tethered carbodiolate 10. The non-tethered carbodiolate 12 was obtained from [Cp*2TiH] and CO2 yielding titanocene formate by reaction of the latter with another equivalent of [Cp*2TiH]. All these carbodiolates contain Ti(III) metal atoms forming electronic triplet states of axial or orthorhombic symmetry. In contrast to the rapidly reacting 1 compound 2 reacts with excess CO2 slowly in m-xylene at 100 °C using only one of its two Ti-CH2 moieties. The structure of the obtained carbodiolate 13 indicates that the primary product analogous to 3 reacts with 2 more rapidly than with CO2.

Early Steps of Glycolonitrile Oligomerization: A Free-Energy Map.

Building on our previous free-energy map (J. Phys. Chem. A 2018, 122, 6769-6779) examining the reactions of monomeric glycolonitrile, we explore the formation of its dimers and trimers in aqueous solution under neutral conditions. While 5-membered rings are kinetically favored, open-chain oligomers with ester or amide linkages are thermodynamically favored. Accessing the 5-membered rings also provides a potential route to glyoxal that bypasses preforming glycolamide, the thermodynamic sink for monomers. However, finding a kinetically accessible route to glycine starting from glycolonitrile in the absence of added ammonia at room temperature proved challenging; the best case involved an intramolecular nucleophilic substitution reaction in a dimer containing neighboring imine and amide groups. Our free-energy map also examines routes to experimentally proposed moieties, explaining why some are observed in low yield or not at all.

Surface-Confined Macrocyclization via Dynamic Covalent Chemistry.

Surface-confined synthesis is a promising approach to build complex molecular nanostructures including macrocycles. However, despite the recent advances in on-surface macrocyclization under ultrahigh vacuum, selective synthesis of monodisperse and multicomponent macrocycles remains a challenge. Here, we report on an on-surface formation of [6 + 6] Schiff-base macrocycles via dynamic covalent chemistry. The macrocycles form two-dimensional crystalline domains on the micrometer scale, enabled by dynamic conversion of open-chain oligomers into well-defined ∼3.0 nm hexagonal macrocycles. We further show that by tailoring the length of the alkyl substituents, it is possible to control which of three possible products-oligomers, macrocycles, or polymers-will form at the surface. In situ scanning tunneling microscopy imaging combined with density functional theory calculations and molecular dynamics simulations unravel the synergistic effect of surface confinement and solvent in leading to preferential on-surface macrocyclization.

Silver compounds based on N,N,N-tridentate pyridylpyrazolate ligands. An opportunity to build cyclic trimetallic and oligomeric luminescent liquid crystals

Silver pyrazolate complexes [Ag(μ-pzR(n)py)]3 [R(n)=C6H4OCnH2n+1; 3 (n=1); 4 (n=10); 5 (n=12); 6 (n=16) and 7 (n=18)] have been prepared by reaction of Ag2O with 3-(4-n-alkyloxyphenyl)-5-(pyridin-2-yl)pyrazole ligands [HpzR(n)py]. The presence of the pyridine as substituent group on the ligand seems to favour the formation of silver cyclic trimers which were isolated in the solid state, as it was supported by the X-ray single crystal structure of the derivative bearing the shortest alkyl chain [Ag(μ-pzR(1)py)]3 (3). By contrast, in CDCl3 or CD2Cl2 solution, the formation of one-dimensional coordination oligomers [Ag(μ-pzR(n)py)]x is proposed. The lability and interchange of AgN pyrazolic bonds of the trimeric structures in polar solvents appear to be responsible for the self-organization of Ag/μ-pzR(n)py motifs into open-chain oligomers. However, in C6D6 solution, the presence of only one set of signals led us to consider that apolar solvents may not affect the AgN pyrazolic bonds, so that the cyclic trimeric structure found in the solid state could be maintained in solution. Complexes bearing the longest chains [5 (n=12); 6 (n=16) and 7 (n=18)] exhibited liquid crystal behaviour showing smectic A (SmA) mesophases in agreement with the open-chain oligomeric structure proposed for the mesomorphic state. Photophysical studies performed on [Ag(μ-pzR(12)py)]3 (5), chosen as a representative example of the series, reveal the presence of luminescence in solution at room temperature for these materials.

Complexes of gold(I) with a chiral diphosphine and bis(pyridine) ligands: Isomeric macrocycles and a polymer

The self-assembly of [Au2(μ-(±)binap)X2], which have weakly coordinated anions X−=trifluoroacetate, triflate or nitrate, with bis(amidopyridyl) ligands (NN) has given three different macrocyclic complexes of general formula [Au4(μ-(±)binap)2(μ-NN)2]X4, an open complex [Au2(μ-(±)binap)(κ1-NN)2]X2, and a polymer [{Au2(μ-(±)binap)(μ-NN)}n]X2n. Macrocycles with both homochiral (RR/SS) and heterochiral (RS/SR) combinations of the two binap ligands in the cations [Au4(μ-binap)2(μ-NN)2]4+ have been structurally characterized. The polymeric complex has the syndiotactic (heterochiral) architecture. The donor ability of the anion X− is shown to affect both the degree of self-assembly in solution, through competition with the bis(amidopyridyl) ligand for coordination to gold(I), and the conformation of the bis(amidopyridyl) ligand in the products, through hydrogen bonding effects. In solution, there is a rapid equilibrium between cyclic and open chain oligomers, as determined by ESI-MS and NMR studies.

Palladium(II)-directed self-assembly of a neutral molecular triangle as a heteroditopic receptor for ion pairs.

A molecular triangle, based on the self-assembly of 4,7-phenanthroline by a neutral palladium complex, has been synthesized and characterized by a combination of techniques: (1)H NMR and UV-vis absorption spectroscopies, mass spectrometry, elemental analysis, and gel permeation chromatography. This new neutral metallocavitand has demonstrated the capacity to host both anionic and cationic guests, thus acting as an open-shaped heteroditopic receptor. Density functional theory calculations have shown that (i) there is no overtension in the assembly of the discrete triangle, which is more stable than open-chain oligomers, (ii) the adducts formed between the triangle and some salts (modeled in the gas phase) are thermodynamically stable, and (iii) two types of cavities coexist in the triangle, which host ions and ion pairs. This easily accessible triangular unit extends further the rational design of model nanoarchitectures in host-guest chemistry with applications in analytical chemistry and multifunctional molecular materials.

Entry point into new trimeric and tetrameric imide-based macrocyclic esters derived from isophthaloyl dichloride and methyl 6-aminonicotinate

The one-step reaction of isophthaloyl dichloride with the 2-aminopyridine derivative (methyl 6-aminonicotinate) yields (i) a trimer-based macrocycle (EsIO)(3) and (ii) a tetramer-based macrocycle (EsIO)(4) in modest isolated synthetic yields (total of 25%), together with (iii) longer open-chain oligomers. The macrocyclization relies on the semi-flexible imide hinge formed by reaction of the 2-amino(pyridine) functional group with two acyl chloride functional groups. The determining factors in macrocycle synthesis are: (a) imide formation using the heteroaromatic ortho-N functionality; (b) the inherent ability of the imide to twist by 85-115° from planarity (as measured by the CO···CO imide torsion angles), thereby providing a hinge for macrocyclic ring closure or potentially (non)helical assembly in oligomer/polymer formation; (c) the conformational flexibility of the isophthaloyl group with meta-related carbonyl groups to twist and adopt either syn or anti conformations, although the syn conformation is observed structurally for all isophthaloyl groups in both (EsIO)(3) (trezimide) and (EsIO)(4) (tennimide) macrocycles.

Entry point into new trimeric and tetrameric imide-based macrocyclic esters derived from isophthaloyl dichloride and methyl 6-aminonicotinate

The one-step reaction of isophthaloyl dichloride with the 2-aminopyridine derivative (methyl 6-aminonicotinate) yields (i) a trimer-based macrocycle (EsIO)3 and (ii) a tetramer-based macrocycle (EsIO)4 in modest isolated synthetic yields (total of 25%), together with (iii) longer open-chain oligomers. The macrocyclization relies on the semi-flexible imide hinge formed by reaction of the 2-amino(pyridine) functional group with two acyl chloride functional groups. The determining factors in macrocycle synthesis are: (a) imide formation using the heteroaromatic ortho-N functionality; (b) the inherent ability of the imide to twist by 85–115° from planarity (as measured by the CO⋯CO imide torsion angles), thereby providing a hinge for macrocyclic ring closure or potentially (non)helical assembly in oligomer/polymer formation; (c) the conformational flexibility of the isophthaloyl group with meta-related carbonyl groups to twist and adopt either syn or anti conformations, although the syn conformation is observed structurally for all isophthaloyl groups in both (EsIO)3 (trezimide) and (EsIO)4 (tennimide) macrocycles.

Silver Pyrazolates as Coordination-Polymer Luminescent Metallomesogens

Silver pyrazolates with columnar liquid-crystal phases that are stable at room temperature have been prepared by reaction of silver nitrate with 3,5-diarylpyrazolates. The complexes consist of open-chain oligomers, despite the fact that the most common structural type for homoleptic coinage metal pyrazolates is the trimeric metallacycle [M(μ-pz)](3). The special characteristics of silver in forming reversible metal-ligand bonds in solution, evidenced experimentally, leads to supramolecular organizations in which the silver cations promote self-organization of the nonmesomorphic pyrazolates into helical 1D polymers that exhibit columnar mesophases. The materials are readily soluble in common organic solvents and are liquid-crystalline over a broader temperature range than their gold counterparts, which are known to form discrete cyclic trinuclear species. Thin films of the silver complexes show luminescence at room temperature. The compounds described here are the first examples of luminescent metallomesogens formed by a main-chain coordination polymer.

Hydration mechanism on a poly(methacrylic acid) film studied by in situ attenuated total reflection infrared spectroscopy

A drastic structure change during a hydration process of a poly(methacrylic acid) (PMAA) film was observed by time-resolved in situ attenuated total reflection infrared (ATR-IR) spectroscopy. Inter- or intra-hydrogen-bonds via side-chain carboxyl groups are formed as cyclic dimers, side-on dimers and linear open chain oligomers including open dimers in a dried PMAA film. By contacting water, the side-chain hydrogen-bonds in PMAA are dissociated instantly, and then the subsequent carboxyl groups which have no hydrogen-bond newly hydrate with water molecules in a side-on form. Quantum chemical calculations (QCCs) using a model monomer of propionic acid (PA) also support the hydrogen-bonded and hydrated structures explored by the ATR-IR spectroscopy. It has been concluded from the present study that the dissociation of hydrogen-bonded and newly created hydrated structures via the carboxyl groups play an important role for the swelling of PMAA in water.

Characterization of Self‐Assembled Metallodendrimers in Solution, in the Gas Phase, and at Air/Solid Interfaces

It is found that 4,4'-bipyridines functionalized in their 3,3'-positions with Fréchet dendrons of 0th to 3rd generation self-assemble with (dppp)M(II) triflates (dppp: bis-(diphenylphosphino)propane; M = Pd, Pt) into metallo-supramolecular squares. They bear a nanometer-sized cavity inside an unpolar dendritic shell. A total of eight amide groups decorate the rims of the cavity connecting the dendrons to the square. Evidence for their formation up to the third generation comes from ESI-FTICR mass spectrometry and NMR experiments. Based on these results, the presence of significant amounts of other polygons or open-chain oligomers can be excluded. Exchange processes have been studied by variable-temperature NMR spectroscopy and by following the ligand exchanges between different squares by mass spectrometry. The ligand exchange is much slower for the Pt(II) squares as compared to their Pd(II) analogs. Visualization of films of these dendrimers using atomic force microscopy (AFM) provides information on their molecular dimensions. After deposition of a square monolayer on the surface, a slow reorganization within this layer is observed which leads to the formation of "tower-like" aggregates and multi-layer formation. The interplay of interactions between the dendrimers and the surface and interactions between different dendrimers are invoked to rationalize the observations.

Improved preparation of racemic 1,2,3,6,7,8,11,12,13-nonamethoxy-10,15-dihydro-5H-tribenzo[a,d,g]cyclononene

Racemic 1,2,3,6,7,8,11,12,13-nonamethoxy-10,15-dihydro-5H-trbibenzo [a,d,g] cyclononene was prepared via trimerization of 3,4,5-trimethoxybenzyl alcohol catalyzed by Lewis acids such as AlCl3, ZnCl2, FeCl3 and SnCl4 in chlorinated solvents. The reaction proceeded smoothly in dichloromethane with SnCl4 as catalyst and gave 54% yield. Some open chain oligomers were also obtained.

Multivariate Curve Resolution Methods Illustrated Using Infrared Spectra of an Alcohol Dissolved in Carbon Tetrachloride

Methods of curve resolution are new tools to meet the demands of effective data analysis in the modern analytical laboratory. Here, we present one way of resolving a data set typical for the chemical laboratory. To illustrate the necessary steps in a successful curve resolution, infrared spectra of an increasing concentration of 1-octanol in carbon tetrachloride are used. The IR spectra change dramatically as the alcohol self-associates and form various types of hydrogen-bonded aggregates. We present a model containing three different alcohol species. The species represent free alcohol monomers, open-chain oligomers, and cyclic oligomers. The number of non- and hydrogen-bonded species giving a unique contribution to the spectral variance is found using chemical rank analysis. The rank analysis is performed on the complete data matrix, as well as on the most interesting regions of the data. This enables the decomposition of the data matrix into spectral and concentration profiles for each species present. The resolution was performed using eigenstructure tracking analysis followed by alternating least squares.

Oligomer and Polymer Formation in Hexamethylcyclotrisiloxane (D3) – Hydrosilane Systems Under Catalysis by tris(pentafluorophenyl)borane

Reactions of hexamethylcyclotrisiloxane, D3, with 1,1,3,3-tetramethyldisiloxane, HMMH, 1,1,1,3,3-pentamethyldisiloxane, HMM, phenyldimethylsilane and phenylmethylsilane catalyzed by tris(pentafluorophenyl)borane were studied. These reactions lead to ring opening of D3 by the SiH reactant producing open chain oligomers with hydrosilane functionality at one or both chain ends. The reactivity of the hydrosilanes toward D3 decreases in the series: PhMeSiH2 > HMMH > PhMe2SiH > HMM. Competitive self-oligomerization of HMMH and HMM also occurs. Primary products of these processes are able to enter into reactions with the SiH and D3 reactants; some also undergo cyclization. Thus, consecutive and competitive processes lead to a series of various oligohomologues. Gas chromatography in conjunction with chemical ionization mass spectroscopy permitted identification of structure and determination of the basic directions of these oligomerization processes. Polysiloxanes of higher molecular weight may be also formed in some of these systems. The reactions, which occur in the systems studied, are rationalized on the basis of the mechanism involving the hydride transfer from silicon to trivalent boron. This includes the transient formation of tertiary trisilyloxonium borate which decomposes by the hydride transfer to one of the silicon atoms of the trisilyloxonium center.

Ozonolysis of tetramethylethylene: characterization of cyclic and open-chain oligoperoxidic products.

The ozonolysis of tetramethylethylene (TME) in solution to high conversion in nonparticipating solvents at -60 degrees C yields predominantly oligoperoxides. For the first time, these products have been characterized using electrospray ionization mass spectrometry (ESI-MS) under soft ionization conditions. The predominant structure formed in reactions carried out in pentane (up to 2.0 M TME) is shown to be the cyclic hexamer of acetone carbonyl oxide (oligocarbonyl oxide with degree of polymerization, n = 6), but cyclic structures with n up to 19 are observed. A small proportion of the oligoperoxides formed are open-chain compounds with end groups that suggest that chain termination of oligocarbonyl oxides can occur through reaction with either water or hydrogen peroxide. Ozonolysis in dried butyl acetate similarly produces mainly cyclic oligoperoxides. However, ozonolyses carried out in undried butyl acetate yield mainly open-chain oligoperoxides, confirming that propagating carbonyl oxide chains are readily terminated by water. Relative amounts of the open-chain oligomers so-formed suggest that undried butyl acetate contains ca. 0.1% w/w water. The ozonolysis of TME in the participating solvent, methanol, at -60 degrees C yields 2-methoxyprop-2-yl hydroperoxide via reaction of acetone carbonyl oxide with methanol; no oligoperoxidic products are formed in this case.

Kinetics and Redox-Sensitive Oligomerisation Reveal Negative Subunit Cooperativity in Tryparedoxin Peroxidase of Trypanosoma brucei brucei

Tryparedoxin peroxidases (TXNPx) are peroxiredoxin-type enzymes that detoxify hydroperoxides in trypanosomatids. Reduction equivalents are provided by trypanothione [T(SH)2] via tryparedoxin (TXN). The T(SH)2-dependent peroxidase system was reconstituted from TXNPx and TXN of T. brucei brucei (TbTXN-Px and TbTXN). TbTXNPx efficiently reduces organic hydroperoxides and is specifically reduced by TbTXN, less efficiently by thioredoxin, but not by glutathione (GSH) or T(SH)2. The kinetic pattern does not comply with a simple rate equation but suggests negative co-operativity of reaction centers. Gel permeation of oxidized TbTXNPx yields peaks corresponding to a decamer and higher aggregates. Electron microscopy shows regular ring structures in the decamer peak. Upon reduction, the rings tend to depolymerise forming open-chain oligomers. Co-oxidation of TbTXNPx with TbTXNC43S yields a dead-end intermediate mimicking the catalytic intermediate. Its size complies with a stoichiometry of one TXN per subunit of TXNPx. Electron microscopy of the intermediate displays pentangular structures that are compatible with a model of a decameric TbTXNPx ring with ten bound TbTXN molecules. The redox-dependent changes in shape and aggregation state, the kinetic pattern and molecular models support the view that, upon oxidation of a reaction center, other subunits adopt a conformation that has lower reactivity with the hydroperoxide.

M-Diethynylbenzene macrocycles: syntheses and self-association behavior in solution.

m-Diethynylbenzene macrocycles (DBMs), buta-1,3-diyne-bridged [4(n)]metacyclophanes, have been synthesized and their self-association behaviors in solution were investigated. Cyclic tetramers, hexamers, and octamers of DBMs having exo-annular octyl, hexadecyl, and 3,6,9-trioxadecyl ester groups were prepared by intermolecular oxidative coupling of dimer units or intramolecular cyclization of the corresponding open-chain oligomers. The aggregation properties were investigated by two methods, the (1)H NMR spectra and the vapor pressure osmometry (VPO). Although some discrepancies were observed between the association constants obtained from the two methods, the qualitative view was consistent with each other. The analysis of self-aggregation by VPO revealed unique aggregation behavior of DBMs in acetone and toluene, which was not elucidated by the NMR method. Namely, the association constants for infinite association are several times larger than the dimerization constant, suggesting that the aggregation is enhanced by the formation of dimers (a nucleation mechanism). In polar solvents, DBMs aggregate more strongly than in chloroform due to the solvophobic interactions between the macrocyclic framework and the solvents. Moreover, DBMs self-associate in aromatic solvents such as toluene and o-xylene more readily than in chloroform. In particular, the hexameric DBM having a large macrocyclic cavity exhibits extremely large association constants in aromatic solvents. By comparing the aggregation properties of DBMs with the corresponding acyclic oligomers, the effect of the macrocyclic structure on the aggregation propensity was clarified. Finally, it turned out that DBMs tend to aggregate more readily than the corresponding phenylacetylene macrocycles, acetylene-bridged [2(n)]metacyclophanes, owing to the withdrawal of the electron density from the aromatic rings by the butadiyne linkages which facilitates pi-pi stacking interactions.

Adsorption of Benzyl Alcohol onto Alumina and Kaolinite Surfaces from a Nonaqueous Solution

Adsorption of benzyl alcohol from carbon tetrachloride solutions onto alumina and kaolinite is investigated by ultraviolet spectroscopy for analysis of alcohol content. The adsorption isotherms are produced and adsorption mechanisms are discussed by taking into account the self-association of the alcohol molecules. Both isotherms show well-defined plateau sections corresponding to an alcohol packing density of about 0.54 nm2 per molecule. This area is sufficient for the molecules to be adsorbed in a vertical orientation, but with the benzene ring lying along the plane of the interface. If this is the situation, the formation of multilayers as observed above an alcohol concentration of 0.04 mol/kg may occur by stacking of the benzene rings. The stability of such a configuration is achieved by sharing the π-electrons. However, self-association of alcohol molecules to form open chain and cyclic oligomers may affect the formation of multilayers on the minerals. Although the open chain aggregates do have unsaturated valencies for forming hydrogen bonds with the mineral surface, this is not the case for cyclic alcohol aggregates. The open chain oligomers may therefore compete with free alcohol monomers for available sites on the mineral. Thus, data show that the situation caused by self-association of benzyl alcohol should be taken into consideration when adsorption mechanisms are discussed.