Browse
Submit Data
Databases
API
Help

Dataset Information

16 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Theoretical Investigation of the Fusion Process of Mono-Cages to Tri-Cages with CH₄/C₂H₆ Guest Molecules in sI Hydrates.

ABSTRACT: Owing to a stable and porous cage structure, natural gas hydrates can store abundant methane and serve as a potentially natural gas resource. However, the microscopic mechanism of how hydrate crystalline grows has not been fully explored, especially for the structure containing different guest molecules. Hence, we adopt density functional theory (DFT) to investigate the fusion process of structure I hydrates with CH₄/C₂H₆ guest molecules from mono-cages to triple-cages. We find that the volume of guest molecules affects the stabilities of large (5¹²6², L) and small (5¹², s) cages, which are prone to capture C₂H₆ and CH₄, respectively. Mixed double cages (small cage and large cage) with the mixed guest molecules have the highest stability and fusion energy. The triangular triple cages exhibit superior stability because of the three shared faces, and the triangular mixed triple cages (large-small-large) structure with the mixed guest molecules shows the highest stability and fusion energy in the triple-cage fusion process. These results can provide theoretical insights into the growth mechanism of hydrates with other mono/mixed guest molecules for further development and application of these substances.

SUBMITTER: Wei S

PROVIDER: S-EPMC8659103 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Temperature effects on the C-H symmetric stretching vibrational frequencies of guest hydrocarbon molecules in 512, 51262 and 51264 cages of sI and sII clathrate hydrates.

Project description:C-H symmetric stretching vibrational frequencies of CH4, C2H4 and C2H6 molecules encapsulated in 512, 51262 and 51264 cages of structures I (sI) and II (sII) clathrate hydrates measured by Raman spectroscopy in the temperature range of 93-183 K was analysed. The slopes of the symmetric stretch vibrational frequencies under changing temperatures (Δv/ΔT) for CH4, C2H4 and C2H6 molecules encapsulated in sII 51264 cages were smaller than those for molecules in sI 51262 cages, although sI 51262 cages are smaller than sII 51264 cages. We compared the results of Δv/ΔT in this study with the geometrical properties of each host water cage, and these comparisons suggest that the geometry of host water cages affects Δv/ΔT.

| S-EPMC9057130 | biostudies-literature

Absolute configuration and host-guest binding of chiral porphyrin-cages by a combined chiroptical and theoretical approach.

Project description:Porphyrin cage-compounds are used as biomimetic models and substrate-selective catalysts in supramolecular chemistry. In this work we present the resolution of planar-chiral porphyrin cages and the determination of their absolute configuration by vibrational circular dichroism in combination with density functional theory calculations. The chiral porphyrin-cages form complexes with achiral and chiral viologen-guests and upon binding one of the axial enantiomorphs of the guest is bound selectively, as is indicated by induced-electronic-dichroism-spectra in combination with calculations. This host-guest binding also leads to unusual enhanced vibrational circular dichroism, which is the result of a combination of phenomena, such as rigidification of the host and guest structures, charge transfer, and coupling of specific vibration modes of the host and guest. The results offer insights in how the porphyrin cage-compounds may be used to construct a future molecular Turing machine that can write chiral information onto polymer chains.

| S-EPMC7508876 | biostudies-literature

Heterotrimetallic Double Cavity Cages: Syntheses and Selective Guest Binding.

Project description:A strategy for the generation of heterotrimetallic double cavity (DC) cages [Pdn Ptm L4 ]6+ (DC1: n=1, m=2; and DC2: n=2, m=1) is reported. The DC cages were generated by combining an inert platinum(II) tetrapyridylaldehyde complex with a suitably substituted pyridylamine and PdII ions. 1 H and DOSY nuclear magnetic resonance spectroscopy (NMR) and electrospray ionization mass spectrometry (ESIMS) data were consistent with the formation of the DC architectures. DC1 and DC2 were shown to interact with several different guest molecules. The structure of DC1, which features two identical cavities, binding two 2,6-diaminoanthraquinone (DAQ) guest molecules was determined by single-crystal X-ray crystallography. In addition, DC1 was shown to bind two molecules of 5-fluorouracil (5-FU) in a statistical (non-cooperative) manner. In contrast, DC2, which features two different cage cavities, was found to interact with two different guests, 5-FU and cisplatin, selectively.

| S-EPMC9310627 | biostudies-literature

Purely Covalent Molecular Cages and Containers for Guest Encapsulation.

Project description:Cage compounds offer unique binding pockets similar to enzyme-binding sites, which can be customized in terms of size, shape, and functional groups to point toward the cavity and many other parameters. Different synthetic strategies have been developed to create a toolkit of methods that allow preparing tailor-made organic cages for a number of distinct applications, such as gas separation, molecular recognition, molecular encapsulation, hosts for catalysis, etc. These examples show the versatility and high selectivity that can be achieved using cages, which is impossible by employing other molecular systems. This review explores the progress made in the field of fully organic molecular cages and containers by focusing on the properties of the cavity and their application to encapsulate guests.

| S-EPMC9413269 | biostudies-literature

Chiral self-sorting and guest recognition of porous aromatic cages.

Project description:The synthesis of ultra-stable chiral porous organic cages (POCs) and their controllable chiral self-sorting at the molecular and supramolecular level remains challening. Herein, we report the design and synthesis of a serial of axially chiral porous aromatic cages (PAC 1-S and 1-R) with high chemical stability. The theoretical and experimental studies on the chiral self-sorting reveal that the exclusive self-recognition on cage formation is an enthalpy-driven process while the chiral narcissistic and self-sorting on supramolecular assembly of racemic cages can be precisely regulated by π-π and C-H…π interactions from different solvents. Regarding the chemical stability, the crystallinity of PAC 1 is maintained in aqueous solvents, such as boiling water, high-concentrated acid and alkali; mixtures of solvents, such as 1 M H2SO4/MeOH/H2O solution, are also tolerated. Investigations on the chiral sensing performance show that PAC 1 enables enantioselective recognition of axially chiral biaryl molecules.

| S-EPMC9273608 | biostudies-literature

Effect of temperature and large guest molecules on the C-H symmetric stretching vibrational frequencies of methane in structure H and I clathrate hydrates.

Project description:Large molecules such as 2-methylbutane (C5H12) or 2,2-dimethylbutane (C6H14) form structure H (sH) hydrates with methane (CH4) as a help gas. In this study, the Raman spectra of the C-H symmetric stretch region of CH4 enclathrated within various sH hydrates and structure I CH4 hydrates were analyzed in the temperature range 137.7-205.4 K. Thermal expansions of these sH hydrate samples were also measured using powder X-ray diffraction. Symmetric stretch vibrational frequencies of CH4 in host-water cages increased because of varying temperature, and the sizes of the host-water cages also increased; variation of CH4 in small cages was less than in larger cages. Comparing the variations of the C-H symmetric stretching frequencies of CH4 in gas hydrates with varying pressure and temperature, we suggest that the observed trend is caused by thermal vibrations of the CH4 molecule in water cages.

| S-EPMC9053386 | biostudies-literature

Allosteric Guest Binding in Chiral Zirconium(IV) Double Decker Porphyrin Cages.

Project description:Chiral zirconium(IV) double cage sandwich complex Zr(1)2 has been synthesized in one step from porphyrin cage H21. Zr(1)2 was obtained as a racemate, which was resolved by HPLC and the enantiomers were isolated in >99.5 % ee. Their absolute configurations were assigned on the basis of X-ray crystallography and circular dichroism spectroscopy. Vibrational circular dichroism (VCD) experiments on the enantiomers of Zr(1)2 revealed that the chirality around the zirconium center is propagated throughout the whole cage structure. The axial conformational chirality of the double cage complex displayed a VCD fingerprint similar to the one observed previously for a related chiral cage compound with planar and point chirality. Zr(1)2 shows fluorescence, which is quenched when viologen guests bind in its cavities. The binding of viologen and dihydroxybenzene derivatives in the two cavities of Zr(1)2 occurs with negative allostery, the cooperativity factors α (=4 K2/K1) being as low as 0.0076 for the binding of N,N'-dimethylviologen. These allosteric effects are attributed to a pinching of the second cavity as a result of guest binding in the first cavity.

| S-EPMC7898692 | biostudies-literature

Chiral Self-Discrimination and Guest Recognition in Helicene-Based Coordination Cages.

Project description:Chiral nanosized confinements play a major role for enantioselective recognition and reaction control in biological systems. Supramolecular self-assembly gives access to artificial mimics with tunable sizes and properties. Herein, a new family of [Pd2 L4 ] coordination cages based on a chiral [6]helicene backbone is introduced. A racemic mixture of the bis-monodentate pyridyl ligand L1 selectively assembles with PdII cations under chiral self-discrimination to an achiral meso cage, cis-[Pd2 L1P 2 L1M 2 ]. Enantiopure L1 forms homochiral cages [Pd2 L1P/M 4 ]. A longer derivative L2 forms chiral cages [Pd2 L2P/M 4 ] with larger cavities, which bind optical isomers of chiral guests with different affinities. Owing to its distinct chiroptical properties, this cage can distinguish non-chiral guests of different lengths, as they were found to squeeze or elongate the cavity under modulation of the helical pitch of the helicenes. The CD spectroscopic results were supported by ion mobility mass spectrometry.

| S-EPMC6563462 | biostudies-literature

Host-Guest Chemistry of Truncated Tetrahedral Imine Cages with Ammonium Ions.

Project description:Three shape-persistent [4+4] imine cages with truncated tetrahedral geometry with different window sizes were studied as hosts for the encapsulation of tetra-n-alkylammonium salts of various bulkiness. In various solvents the cages behave differently. For instance, in dichloromethane the cage with smallest window size takes up NEt4 + but not NMe4 +, which is in contrast to the two cages with larger windows hosting both ions. To find out the reason for this, kinetic experiments were carried out to determine the velocity of uptake but also to deduce the activation barriers for these processes. To support the experimental results, calculations for the guest uptakes have been performed by molecular mechanics' simulations. Finally, the complexation of pharmaceutical interested compounds, such as acetylcholine, muscarine or denatonium have been determined by NMR experiments.

| S-EPMC6996569 | biostudies-literature

Capture of Singlet Oxygen Modulates Host-Guest Behavior of Coordination Cages.

Project description:The anthracene panels of two tetrahedral MII 4 L6 cages, where MII =CoII or FeII , were found to react with photogenerated singlet oxygen (1 O2 ) in a hetero-Diels-Alder reaction. ESI-MS analysis showed the cobalt(II) cages to undergo complete transformation of all anthracene panels into endoperoxides, whereas the iron(II) congeners underwent incomplete conversion. The reaction was found to be partially reversible in the case of the 1-FeII cage. The dioxygen-cage cycloadducts were found to bind a set of guest molecules more weakly than the parent cages, with affinity dropping by more than two orders of magnitude in some cases. The light-driven cycloaddition reaction between cage and 1 O2 thus served as a stimulus for guest release and reuptake.

| S-EPMC10952966 | biostudies-literature