Cyclic Trimer Research Articles

Formation of Paraldehyde (C6H12O3) in Interstellar Analog Ices of Acetaldehyde Exposed to Ionizing Radiation.

Acetaldehyde (CH3CHO) plays a crucial role in the synthesis of prebiotic molecules such as amino acids, sugars, and sugar-related compounds, and in the progress of chain reaction polymerization in deep space. Here, we report the first formation of the cyclic acetaldehyde trimer - paraldehyde (C6H12O3) - in low-temperature interstellar analog ices exposed to energetic irradiation as proxies of galactic cosmic rays (GCRs). Utilizing vacuum ultraviolet photoionization reflectron time-of-flight mass spectrometry and isotopic substitution experiments, paraldehyde was identified in the gas phase during the temperature-programmed desorption of the irradiated acetaldehyde ices based on the calculated adiabatic ionization energies and isomer-specific dissociative fragmentation patterns upon photoionization. As acetaldehyde is ubiquitous throughout the interstellar medium and has been tentatively identified in interstellar ices, paraldehyde could have formed in acetaldehyde-containing ices in a cold molecular cloud and is an excellent candidate for gas-phase observation in star-forming regions via radio telescopes. The identification of paraldehyde in the gas phase from the processed acetaldehyde ices advances our understanding of how complex organic molecules can be synthesized through polymerization reactions in extraterrestrial ices exposed to GCRs.

Front Cover: Synthesis and Characterization of a Cyclic Trimer of a Chiral Spirosilabifluorene (Chem. Eur. J. 45/2024)

Front Cover: Synthesis and Characterization of a Cyclic Trimer of a Chiral Spirosilabifluorene (Chem. Eur. J. 45/2024)

Revisiting the IR Spectra of H2S in an Argon Matrix: Identification of (H2S)n (n ≤ 4) Clusters via the Spectral Assignment of νS-H Transitions.

Small-molecular clusters of H2S up to tetramer have been experimentally identified in a cold and solid argon matrix by the spectral assignment of νS-H fundamental transitions for different H2S:argon mixing ratios. Normal-mode frequency calculations at the MP2-CP/aug-cc-pV(Q + d)Z level have been used to support the spectral assignments. In addition, modulations in relative populations of different clusters due to the annealing of the deposited matrix and the preheating of the H2S-argon gas mixture before deposition reinforced the spectral assignments. Variations in mixing ratio, annealing of the matrix, and preheating of the gas mixture have also been used, in a combined manner, to unambiguously identify the ν1 and ν3 bands of the H2S monomer, which has been a matter of dispute for a long period. The two bands have been identified at 2634.4 and 2648.0 cm-1, respectively, while three bands at 2581.5, 2568.4, and 2547.6 cm-1 have been assigned to H-bonded dimers, cyclic trimers, and cyclic tetramers, respectively. Multiple bands within 2550-2580 cm-1 have been assigned to caged tetramers. The cooperative strengthening of S-H···S H bonds in cyclic H2S clusters was evident from the linear increment in νS-H spectral shifts with cluster size.

Synthesis and Characterization of a Cyclic Trimer of a Chiral Spirosilabifluorene.

A chiral shape-persistent macrocyclic compound (Si-[3]), designed by the C/Si substitution in the spiro-atom of spirobifluorene in the cyclic trimer (C-[3]), has been successfully synthesized in this study. The C/Si substitution made the spiro-conjugation and energy levels of HOMO and LUMO decrease. Due to the silicon substitution, the macrocyclic compound Si-[3] was able to be degraded by fluoride ions, but its reaction rate was slower than that of the unsubstituted spirosilabifluorene, showing the chemical stability of Si-[3]. Furthermore, the chiroptical properties of Si-[3] with D3-symmetric macrocyclic structure were investigated, and (P,P,P)-Si-[3] showed a high emission quantum yield (Φf=80 %) and moderate dissymmetry factor of circularly polarized luminescence (CPL) (glum,exp=-1.2×10-3). According to the time-dependent density-functional theory (TD-DFT) calculations using polarizable continuum model (PCM), the bright CPL from Si-[3] was explained by a planarization of one bisilafluorenyl moiety at the excited state, which is responsible for the almost fully-allowed radiative transition with a short emission lifetime of τf=1.89 ns.

Hydrogen- and halogen-bonding-directed trimeric supramolecular motifs in dihalogenated 1,2,4-triazoles.

Hydrogen-bonding and halogen-bonding interactions are important noncovalent interactions that play a significant role in the crystal structure of organic molecules. An in-depth analysis is given of the crystal packing of two previously reported crystal structures of dihalogenated 1,2,4-triazole derivatives, namely 3,5-dichloro-1H-1,2,4-triazole and 3,5-dibromo-1H-1,2,4-triazole. This work provides insights into the complex interplay of hydrogen-bonding and halogen-bonding interactions resulting in the formation of multiple trimeric motifs in the crystal structure of 1,2,4-triazole derivatives. Analysis of the crystal packing of these isostructural crystal structures revealed that the molecular arrangement in these molecules is primarily stabilized by the formation of different trimeric motifs stabilized by N-H...N hydrogen bonds, N-H...X (X = Cl/Br) halogen bonds and C-X...X halogen-bonding interactions. Computational studies further revealed that all these trimers are energetically stable. A crystallographic database search further reveals that while the cyclic trimers reported in this study are present in other molecules, structures analyzed in this study are the sole instances where all are present simultaneously.

Separation and Identification of Molecular Species by GC-MS for the Reaction Mixture with Methyltrimethoxysilane (MTMOS)

This article aimed to separate and identify molecular species obtained in the sol-gel process by gas chromatography coupled with mass spectrometry (GC-MS), for the reaction mixture with methyltrimethoxysilane (MTMOS). In the presence of an unhydrolyzed methyl group, the molecular species starting with the cyclic trimers, a series of geometric isomers were separated and identified due to the position of the methyl groups in relation to the ring plane of each siloxane molecule; in addition, for the hydrolyzed products, isomers with different relative positions of the hydroxyl groups to the methyl and methoxy groups were separated and identified. The reactivity of the new molecular species formed determines subsequent stages of the sol-gel process.

Synthesis and Structural Characterization of Macrocyclic α-ABpeptoids and Their DNA-Encoded Library.

The first synthesis of macrocyclic α-ABpeptoids with varying lengths is described. X-ray crystal structures reveal that cyclic trimer displays a chair-like conformation with a cct amide sequence and cyclic tetramer has a saddle-like structure with an uncommon cccc amide arrangement. The creation of a DNA-encoded combinatorial library of macrocyclic α-ABpeptoids is described.

Hierarchical Self‐Assembly of Curved Aromatics: From Donor–Acceptor Porphyrins to Triply Periodic Minimal Surfaces

AbstractA saddle‐shaped π‐extended zinc porphyrin containing a peripheral pyridyl ligand undergoes quantitative self‐assembly into a cyclic trimer. The trimer has a prismatic structure with negatively curved side walls, which promote the formation of supramolecular organic frameworks stabilized by dispersion interactions. The first framework type, UWr‐1, has the npo topology, with a hexagonal structure analogous to the Schwartz H triply periodic minimal surface. Co‐crystallization of the trimer with either C60 and C70 produces the isomorphous cubic UWr‐2 and UWr‐3 phases, characterized by the ctn network topology and a structural relationship to the Fischer‐Koch minimal surface S. All three phases contain complex labyrinths of solvent‐filled channels, corresponding to very large probe‐accessible volumes (68 % to 76 %). The UWr‐2 network could be partly desolvated while retaining its long range dimensional order, indicating remarkable strength of the dispersion interactions in the crystal. A theoretical analysis of noncovalent interactions shows the role of geometrical matching between the negatively curved porphyrin units and positively curved fullerenes.

Hierarchical Self-Assembly of Curved Aromatics: From Donor-Acceptor Porphyrins to Triply Periodic Minimal Surfaces.

A saddle-shaped π-extended zinc porphyrin containing a peripheral pyridyl ligand undergoes quantitative self-assembly into a cyclic trimer. The trimer has a prismatic structure with negatively curved side walls, which promote the formation of supramolecular organic frameworks stabilized by dispersion interactions. The first framework type, UWr-1, has the npo topology, with a hexagonal structure analogous to the Schwartz H triply periodic minimal surface. Co-crystallization of the trimer with either C60 and C70 produces the isomorphous cubic UWr-2 and UWr-3 phases, characterized by the ctn network topology and a structural relationship to the Fischer-Koch minimal surface S. All three phases contain complex labyrinths of solvent-filled channels, corresponding to very large probe-accessible volumes (68 % to 76 %). The UWr-2 network could be partly desolvated while retaining its long range dimensional order, indicating remarkable strength of the dispersion interactions in the crystal. A theoretical analysis of noncovalent interactions shows the role of geometrical matching between the negatively curved porphyrin units and positively curved fullerenes.

Oligomer composition and content in regenerated PA6 fiber and its effect on properties

AbstractThe preparation process from waste fibers to regenerated fibers is an environmental significance work. In this work, liquid chromatography/time‐of‐flight mass spectrometry, advanced polymer chromatography/multi‐angle laser‐light‐scattering/refractive index detector, and two‐dimensional wide‐angle X‐ray diffractometry were employed to characterize the polycaprolactam(PA6) fibers above oligomers composition and content, molecular weight and distribution, crystallization and orientation, and analyzing the changes in mechanical properties. The total content of oligomers in physical and chemical regenerated PA6 fiber is 2.084 wt% and 1.812 wt%, individually, which is higher than that in waste PA6 fiber. And the oligomer content of C1–C4 (cyclic monomer, cyclic dimer, cyclic trimer, and cyclic tetramer) in the regenerated PA6 fiber is higher than that of waste PA6 fiber. The regenerated PA6 fiber sample contains more low‐molecular‐weight substances, making it easier to form crystal nuclei and crystallize. During the dyeing process of the regenerated PA6 fiber, the γ crystal transformed into α crystal. The tensile strength of physical and chemical regenerated PA6 fiber is lower than that of waste PA6 fiber. And after dyeing, the oligomers content of regenerated PA6 fiber is significantly decreased, especially in C1–C4 oligomer. However, the crystalliniy and orientation of regenerated PA6 fibers were improved, which also leads to the fracture strength increased by about 20% compared to undyed fibers.

The ubiquitous P(o-tol)3 ligand promotes formation of catalytically-active higher order palladacyclic clusters.

The Herrmann-Beller catalyst, Pd[(C^P)(μ2-OAc)]2, is readily formed by reaction of the cyclic trimer of 'Pd(OAc)2' with P(o-tol)3. In the presence of hydroxide, Pd(C^P)(μ2-OAc)]2 converts to [Pd(C^P)(μ 2 -OH)]2. Here, we report how this activated Pd precatalyst species, and related species, serve as a conduit for formation of higher order Pd n clusters containing multiple cyclopalladated P(o-tol)3 ligands. The catalytic competency of a Pd4-palladacyclic cluster is demonstrated in an arylated Heck cross-coupling, which is comparable to the base-activated form of Herrmann's catalyst, namely [Pd(C^P)(μ2-OH)]2. The findings show that 'simple' ubiquitous phosphine ligands can promote higher order Pd speciation, moving beyond well-known phosphine-ligated Pd1 and Pd2 complexes. The findings challenge the status quo in the field, in that phosphine ligands can ligate higher order Pd n species which are catalytically competent species in cross-coupling reactions.

Synthesis and Photocatalytic CO2 Reduction of a Cyclic Zinc(II) Porphyrin Trimer with an Encapsulated Rhenium(I) Bipyridine Tricarbonyl Complex.

We previously reported a cyclic Zn(II) porphyrin trimer in which three Zn porphyrins are alternately bridged by three 2,2'-bipyridine (bpy) moieties, enabling the encapsulation of metal complexes within the nanopore formed by the Zn porphyrins. In this study, we introduced a [Re(CO)3 Br] fragment into one of the bpy moieties of the cyclic trimer to form the catalytic Re(4,4'-R2 -bpy)(CO)3 Br center (R=methyl ester). The ester groups (R) play an important role in the synthesis of the cyclic structure. However, it was observed that these ester groups significantly deactivated the photocatalytic CO2 reduction reaction. Therefore, we converted the ester groups with a suitable reducing reagent into hydroxymethyl groups, followed by acetylation to form acetoxymethyl groups. This modification remarkably enhanced the photocatalytic activity of the cyclic trimer=Re complex system for CO2 reduction. Moreover, in the modified system, the presence of the Re complex induced room-temperature phosphorescence of the Zn porphyrin. The phosphorescence was significantly quenched by 1,3-dimethyl-2-phenyl-2,3-dihydro-1H-benzo[d]imidazole, indicating that efficient electron transfer mediated by the excited triplet state of the Zn porphyrin occurs during the photocatalytic CO2 reduction.

Insight into the Binding of Argon to Cyclic Water Clusters from Symmetry-Adapted Perturbation Theory.

This work systematically examines the interactions between a single argon atom and the edges and faces of cyclic H2O clusters containing three-five water molecules (Ar(H2O)n=3-5). Full geometry optimizations and subsequent harmonic vibrational frequency computations were performed using MP2 with a triple-ζ correlation consistent basis set augmented with diffuse functions on the heavy atoms (cc-pVTZ for H and aug-cc-pVTZ for O and Ar; denoted as haTZ). Optimized structures and harmonic vibrational frequencies were also obtained with the two-body-many-body (2b:Mb) and three-body-many-body (3b:Mb) techniques; here, high-level CCSD(T) computations capture up through the two-body or three-body contributions from the many-body expansion, respectively, while less demanding MP2 computations recover all higher-order contributions. Five unique stationary points have been identified in which Ar binds to the cyclic water trimer, along with four for (H2O)4 and three for (H2O)5. To the best of our knowledge, eleven of these twelve structures have been characterized here for the first time. Ar consistently binds more strongly to the faces than the edges of the cyclic (H2O)n clusters, by as much as a factor of two. The 3b:Mb electronic energies computed with the haTZ basis set indicate that Ar binds to the faces of the water clusters by at least 3 kJ mol-1 and by nearly 6 kJ mol-1 for one Ar(H2O)5 complex. An analysis of the interaction energies for the different binding motifs based on symmetry-adapted perturbation theory (SAPT) indicates that dispersion interactions are primarily responsible for the observed trends. The binding of a single Ar atom to a face of these cyclic water clusters can induce perturbations to the harmonic vibrational frequencies on the order of 5 cm-1 for some hydrogen-bonded OH stretching frequencies.

Preparation and Properties of Phenolic Epoxy Modified Silicone Resin

Phenolic epoxy resin (F51) was first reacted with silane coupling agent (3-aminopropyl)triethoxysilane (KH550) to form a silanized phenolic epoxy resin (SPER); then the SPER was copolymerized with methylphenyl silicone resin (MPS) to synthesize phenolic epoxy modified silicone copolymer (PEMSC). The chemical structure of the PEMSC was characterized by FT-IR. The results of tensile strength and shear strength measurements indicated that the successful introduction of F51 significantly improved the mechanical and adhesive properties of the PEMSC; compared with the PEMSC with 10 phr of F51 added, the tensile strength and shear strength of the PEMSC with 40 phr increased by 8.5 and 3.5 times respectively. The TGA and DTGA analysis showed that the initial thermal decomposition temperature and the residual weight of PEMSC at 800 °C decreased compared to MPS, but the temperature corresponding to the maximum thermal decomposition rate in the second stage increased. Qualitative analysis was conducted on the decomposition products of PEMSC using gas chromatography coupled with mass spectrometry (GC-MS). The results showed that the relative content of aromatic hydrocarbons and their derivatives in the decomposition products of PEMSC was 64.11%, and the relative content of cyclic trimers and higher cyclomers was 20.41%.

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.

Analysis of Migrant Cyclic PET Oligomers in Olive Oil and Food Simulants Using UHPLC-qTOF-MS.

Oligomers are a particular category of non-intentionally added substances (NIAS) that may be present in food contact materials (FCMs), such as polyethylene terephthalate (PET), and consequently migrate into foods. Here, an ultra-high-pressure liquid chromatography quadruple time-of-flight mass spectrometry (UHPLC-qTOF-MS) method was developed for the analysis of 1st series cyclic PET oligomers in virgin olive oil (VOO) following a QuEChERS clean-up protocol. Oligomer migration was evaluated with two different migration experiments using bottles from virgin and recycled PET: one with VOO samples stored in household conditions for a year and one using the food simulant D2 (95% v/v ethanol in water) at 60 °C for 10 days. Calibration curves were constructed with fortified VOO samples, with the LOQs ranging from 10 to 50 µg L-1 and the recoveries ranging from 86.6 to 113.0%. Results showed no migration of PET oligomers in VOO. However, in the simulated study, significant amounts of all oligomers were detected, with the migration of cyclic PET trimers from recycled bottles being the most abundant. Additional substances were tentatively identified as linear derivatives of PET oligomers. Again, open trimer structures in recycled bottles gave the most significant signals.

Dispersion, Rehybridization, and Pentacoordination: Keys to Understand Clustering of Boron and Aluminum Hydrides and Halides.

The structure, stability, and bonding characteristics of dimers and trimers involving BX3 and AlX3 (X = H, F, Cl) in the gas phase, many of them explored for the first time, were investigated using different DFT (B3LYP, B3LYP/D3BJ, and M06-2X) and ab initio (MP2 and G4) methods together with different energy decomposition formalisms, namely, many-body interaction-energy and localized molecular orbital energy decomposition analysis. The electron density of the clusters investigated was analyzed with QTAIM, electron localization function, NCIPLOT, and adaptive natural density partitioning approaches. Our results for triel hydride dimers and Al2X6 (X = F, Cl) clusters are in good agreement with previous studies in the literature, but in contrast with the general accepted idea that B2F6 and B2Cl6 do not exist, we have found that they are predicted to be weakly bound systems if dispersion interactions are conveniently accounted for in the theoretical schemes used. Dispersion interactions are also dominant in both homo- and heterotrimers involving boron halide monomers. Surprisingly, B3F9 and B3Cl9 C3v cyclic trimers, in spite of exhibiting rather strong B-X (X = F, Cl) interactions, were found to be unstable with respect to the isolated monomers due to the high energetic cost of the rehybridization of the B atom, which is larger than the two- and three-body stabilization contributions when the cyclic is formed. Another important feature is the enhanced stability of both homo- and heterotrimers in which Al is the central atom because Al is systematically pentacoordinated, whereas this is not the case when the central atom is B, which is only tri- or tetra-coordinated.

The behavior of water molecules in the nanocavities of the HKUST-1 framework: A combined quantum mechanical and vibrational spectroscopy investigation

We have investigated the host/guest molecular interactions and the H-bonding clustering in the H2O/HKUST-1 system. In-situ Fourier transform infrared spectroscopy was the experimental technique used to gather information at the molecular level. Measurements collected under sorption equilibrium conditions and in a dynamic regime were interpreted with the aid of a detailed QM vibrational analysis of the host/guest adduct and of a series of H2O clusters. The local arrangement of the adduct formed by H2O and the coordinatively unsaturated sites was characterized in terms of structure and interaction energy, and signatures for this adduct were predicted by theory in the ν(OH) range and experimentally confirmed. Within the metal organic framework nanocavities, six-membered water clusters having specific conformations were found to be the prevailing species. Cyclic trimers were also identified, their stabilization being ascribed to nanoconfining effects. The analysis of the δ(HOH) range elucidated the nature of the complex band shape and confirmed the results obtained in the ν(OH) interval. Low-temperature measurements allowed us to exclude the crystallization of the water clusters in the nanocavities.

Hierarchical Supramolecular Nanostructures of Cyclic Hydrogen-Bonding Catemers in Dibenzo[a,c]phenazinecarboxylic Acid Discotic Liquid Crystals

AbstractThe hydrogen-bonding motif of dibenzo[a,c]phenazinecarboxylic acids can be enforced to form hierarchical cyclic hydrogen-bonded trimers for creating a 3D Colh assembly at the mesophase, as demonstrated by X-ray diffraction. Scanning tunneling microscopy was used to characterize the formation of the cyclic trimers. Atomic force microscopy revealed the formation of nanopillars on a hydrophilized silica surface upon annealing from isotropic to room temperature.

Two-step degradable ABAC-type periodic poly(cyclic acetal)s synthesized by sequence-programmed monomer formation and subsequent polyaddition based on cyclotrimerization of one vinyl monomer and two aldehydes

ABAC-type periodic poly(cyclic acetal)s were synthesized via a two-step method consisting of the synthesis of a sequence-programmed cyclic trimers from one vinyl monomer and two bifunctional aldehydes (isophthalaldehyde or terephthalaldehyde) and the successive cyclotrimerization of the cyclic trimer with another vinyl monomer. The use of 1,1-diphenylethylene (DPE) was important for synthesizing the cyclic trimer in high yield because the successive cyclotrimerization and other side reactions were suppressed due to the steric hindrance of DPE. The ABA-type sequence-programmed cyclic trimer consisting of one DPE molecule (unit B) and two dialdehydes (unit A) possesses two unreacted aldehyde moieties; hence, the cyclic trimer successfully underwent successive cyclotrimerization with vinyl ethers (VEs) (unit C), such as 2-chloroethyl VE (CEVE) and ethyl 2-methyl-1-propenyl ether (EMPE). As a result, ABAC-type periodic poly(cyclic acetal)s with alternately arranged two phenyl rings and VE-derived side chains were produced. The two types of cyclic acetal structures in the main chain exhibited different acid degradability. Indeed, the CEVE-derived cyclic acetal structures were selectively degraded under acidic conditions at 60 °C for 15 min, which was followed by the subsequent degradation of the DPE-derived cyclic acetal structures in 24 h. In addition, the ABAC-type periodic polymers exhibited good thermal properties, which were attributed to the cyclic acetal structures.