Determination of NMR Lineshape Anisotropy of Guest Molecules within Inclusion Complexes from Molecular Dynamics Simulations

Nonspherical cages in inclusion compounds can result in non‐uniform motion of guest species in these cages and anisotropic lineshapes in NMR spectra of the guest. Herein, we develop a methodology to calculate lineshape anisotropy of guest species in cages based on molecular dynamics simulations of the inclusion compound. The methodology is valid for guest atoms with spin 1/2 nuclei and does not depend on the temperature and type of inclusion compound or guest species studied. As an example, the nonspherical shape of the structure I (sI) clathrate hydrate large cages leads to preferential alignment of linear CO₂ molecules in directions parallel to the two hexagonal faces of the cages. The angular distribution of the CO₂ guests in terms of a polar angle θ and azimuth angle ? and small amplitude vibrational motions in the large cage are characterized by molecular dynamics simulations at different temperatures in the stability range of the CO₂ sI clathrate. The experimental ¹³C NMR lineshapes of CO₂ guests in the large cages show a reversal of the skew between the low temperature (77 K) and the high temperature (238 K) limits of the stability of the clathrate. We determine the angular distributions of the guests in the cages by classical MD simulations of the sI clathrate and calculate the ¹³C NMR lineshapes over a range of temperatures. Good agreement between experimental lineshapes and calculated lineshapes is obtained. No assumptions regarding the nature of the guest motions in the cages are required.     

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

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.     

非对称笼间电子迁移异构体与电场诱导电子迁移

基于密度泛函理论研究了非对称双笼型单分子溶剂化电子e^-@C₂₄F₂₂(NH)₂C₂₀F₁₈(1、2 和3), 进一步展示了我们提出的一种新型电子异构体——(非对称型的)笼间电子迁移异构体. 1、2 和3 具有显著不同的偶极矩. 由于都存在两个氧化还原中心, 它们属于一种非金属型的新型Robin-Day II-III 分子. 对于1 和3, 额外电子分别定域在C₂₄F₂₂和C₂₀F₁₈笼里(Robin-Day II); 对于2, 额外电子则离域于两个非对称的笼中(Robin-Day III). 值得注意的是, 在y 轴方向上外加-0.0004和-0.0008 a.u.的临界电场(E_c)时可分别使1 的额外电子从C₂₄F₂₂笼中部分和全部地迁移到C₂₀F₁₈笼中, 即实现从1 到2 再到3 的转化; 当E_c为0.0004 a.u.时, 3 的额外电子从C₂₀F₁₈笼中全部迁移到了C₂₄F₂₂笼中, 即3 未经过2 直接转化成了1.     

Raman spectra of vibrational and librational modes in methane clathrate hydrates using density functional theory

The sI type methane clathrate hydrate lattice is formed during the process of nucleation where methane gas molecules are encapsulated in the form of dodecahedron (5(12)CH(4)) and tetrakaidecahedron (5(12)6(2)CH(4)) water cages. The characterization of change in the vibrational modes which occur on the encapsulation of CH(4) in these cages plays a key role in understanding the formation of these cages and subsequent growth to form the hydrate lattice. In this present work, we have chosen the density functional theory (DFT) using the dispersion corrected B97-D functional to characterize the Raman frequency vibrational modes of CH(4) and surrounding water molecules in these cages. The symmetric and asymmetric C-H stretch in the 5(12)CH(4) cage is found to shift to higher frequency due to dispersion interaction of the encapsulated CH(4) molecule with the water molecules of the cages. However, the symmetric and asymmetric O-H stretch of water molecules in 5(12)CH(4) and 5(12)6(2)CH(4) cages are shifted towards lower frequency due to hydrogen bonding, and interactions with the encapsulated CH(4) molecules. The CH(4) bending modes in the 5(12)CH(4) and 5(12)6(2)CH(4) cages are blueshifted, though the magnitude of the shifts is lower compared to modes in the high frequency region which suggests bending modes are less affected on encapsulation of CH(4). The low frequency librational modes which are collective motion of the water molecules and CH(4) in these cages show a broad range of frequencies which suggests that these modes largely contribute to the formation of the hydrate lattice.     

Fabrication of Pillar-Cage Fluorinated Anion Pillared Metal–Organic Frameworks via a Pillar Embedding Strategy and Efficient Separation of SO2 through Multi-Site Trapping

Flue gas desulfurization is crucial for both human health and ecological environments. However, developing efficient SO₂ adsorbents that can break the trade-off between adsorption capacity and selectivity is still challenging. In this work, a new type of fluorinated anion-pillared metal–organic frameworks (APMOFs) with a pillar-cage structure is fabricated through pillar-embedding into a highly porous and robust framework. This type of APMOFs comprises smaller tetrahedral cages and larger icosahedral cages interconnected by embedded [NbOF₅]²⁻ and [TaOF₅]²⁻ anions acting as pillars. The APMOFs exhibits high porosity and density of fluorinated anions, ensuring exceptional SO₂ adsorption capacity and ultrahigh selectivity for SO₂/CO₂ and SO₂/N₂ gas mixtures. Furthermore, these two structures demonstrate excellent stability towards water, acid/alkali, and SO₂ adsorption. Cycle dynamic breakthrough experiments confirm the excellent separation performance of SO₂/CO₂ gas mixtures and their cyclic stability. SO₂-loaded single-crystal X-ray diffraction, Grand canonical Monte Carlo (GCMC) simulations combined with density functional theory (DFT) calculations reveal the preferred adsorption domains for SO₂ molecules. The multiple-site host–guest and guest-guest interactions facilitate selective recognition and dense packing of SO₂ in this hybrid porous material. This work will be instructive for designing porous materials for flue gas desulfurization and other gas-purification processes.     

Distribution of Butane in the Host Water Cage of Structure II Clathrate Hydrates

To understand host–guest interactions of hydrocarbon clathrate hydrates, we investigated the crystal structure of simple and binary clathrate hydrates including butane (n‐C₄H₁₀ or iso‐C₄H₁₀) as the guest. Powder X‐ray diffraction (PXRD) analysis using the information on the conformation of C₄H₁₀ molecules obtained by molecular dynamics (MD) simulations was performed. It was shown that the guest n‐C₄H₁₀ molecule tends to change to the gauche conformation within host water cages. Any distortion of the large 5¹²6⁴ cage and empty 5¹² cage for the simple iso‐C₄H₁₀ hydrate was not detected, and it was revealed that dynamic disorder of iso‐C₄H₁₀ and gauche‐nC₄H₁₀ were spherically extended within the large 5¹²6⁴ cages. It was indicated that structural isomers of hydrocarbon molecules with different van der Waals diameters are enclathrated within water cages in the same way owing to conformational change and dynamic disorder of the molecules. Furthermore, these results show that the method reported herein is applicable to structure analysis of other host–guest materials including guest molecules that could change molecular conformations.     

烷烃客体分子(CnHm, n≤6, m≤14)在51262和51264水笼中的稳定性与拉曼光谱的密度泛函理论计算

可燃冰矿藏中气体成分非常复杂,通过谱学分析对水合物样品成分进行指认具有重要意义.基于B97-D/6-311++G（2d,2p）的密度泛函理论（DFT）计算,我们系统地探索了构成水合物的两种标准水笼（5¹²6²和5¹²6⁴）包络十八种不同烷烃客体分子的稳定性. 从计算结果可以看出,除了3-甲基戊烷和2,3-二甲基丁烷两个烷烃客体分子,其它16个烷烃客体分子都可以被容纳在5¹²6²笼中;但是与5¹²6²笼不同,十八种烷烃客体分子都可以被容纳在尺寸较大的5¹²6⁴笼中. 同时,我们也模拟了五种直链烷烃和四种环状烷烃在5¹²6²和5¹²6⁴笼中相应的谱学特征,从拉曼谱图上可以看出,随着碳原子数量的增多,直链烷烃客体分子C―H键伸缩振动区的多数拉曼谱带向高波数移动,而环状烷烃客体分子C―H键伸缩振动区的拉曼谱带则向低波数移动. 这些结果为实验上通过拉曼谱测量指认水合物矿藏的成分提供理论参考.     

Heterogeneous crystal growth of methane hydrate on its sII [001] crystallographic face

This paper presents a systematic molecular simulation study of the heterogeneous crystal growth of methane hydrate sII from supersaturated aqueous methane solutions. The growth of sII hydrate on the [001] crystallographic face is achieved through utilization of a recently proposed methodology, and rates of crystal growth of 1 A/ns were sustained for the molecular models and specific conditions employed in this work. Characteristics of the crystals grown as well as properties and structure of the interface are examined. Water cages with a 5(12)6(3) arrangement, which are improper to both sI and sII structures, are identified during the heterogeneous growth of sII methane hydrate. We show that the growth of a [001] face of sII hydrate can produce an sI crystalline structure, confirming that cross-nucleation of methane hydrate structures is possible. Defects consisting of two methane molecules trapped in large 5(12)6(4) cages and water molecules trapped in small and large cages are observed, where in one instance we have found a large 5(12)6(4) cage containing three water molecules.     

Temperature- and Pressure-induced Structural Transition of Binary Clathrate Hydrates

We discover new structure II (sII) hydrate forming agents of two C₄H₈O molecules (2-methyl-2-propen-1-ol and 2-butanone) and report the abnormal structural transition of binary C₄H₈O+CH₄ hydrates between structure I (sI) and sII with varying temperature and pressure conditions. In both (2-methyl-2-propen-1-ol+CH₄) and (2-butanone+CH₄) systems, the phase boundary of the two different hydrate phases (sI and sII) exists at the slope change of the phase-equilibrium curve in the semi-logarithmic plots. We confirm the crystal structures of two hydrates synthesized at low (278 K and 6 MPa) and high (286 K and 15 MPa) temperature and pressure conditions by using high-resolution powder diffraction and Raman spectroscopy. 2-Methyl-2-propen-1-ol and 2-butanone can occupy the large cages of sII hydrate at low temperature and pressure conditions; however, they are excluded from the hydrate phase at high temperature and pressure conditions, resulting in the formation of pure sI CH₄ hydrate.     

The cages, dynamics, and structuring of incipient methane clathrate hydrates

Interest in describing clathrate hydrate formation mechanisms spans multiple fields of science and technical applications. Here, we report findings from multiple molecular dynamics simulations of spontaneous methane clathrate hydrate nucleation and growth from fully demixed and disordered two-phase fluid systems of methane and water. Across a range of thermodynamic conditions and simulation geometries and sizes, a set of seven cage types comprises approximately 95% of all cages formed in the nucleated solids. This set includes the ubiquitous 5(12) cage, the 5(12)6(n) subset (where n ranges from 2-4), and the 4(1)5(10)6(n) subset (where n also ranges from 2-4). Transformations among these cages occur via water pair insertions/removals and rotations, and may elucidate the mechanisms of solid-solid structural rearrangements observed experimentally. Some consistency is observed in the relative abundance of cages among all nucleation trajectories. 5(12) cages are always among the two most abundant cage types in the nucleated solids and are usually the most abundant cage type. In all simulations, the 5(12)6(n) cages outnumber their 4(1)5(10)6(n) counterparts with the same number of water molecules. Within these consistent features, some stochasticity is observed in certain cage ratios and in the long-range ordering of the nucleated solids. Even when comparing simulations performed at the same conditions, some trajectories yield swaths of multiple adjacent sI unit cells and long-range order over 5 nm, while others yield only isolated sI unit cells and little long-range order. The nucleated solids containing long-range order have higher 5(12)6(2)/5(12) and 5(12)6(3)/4(1)5(10)6(2) cage ratios when compared to systems that nucleate with little long-range order. The formation of multiple adjacent unit cells of sI hydrate at high driving forces suggests an alternative or addition to the prevailing hydrate nucleation hypotheses which involve formation through amorphous intermediates.     

Balancing Ligand Flexibility versus Rigidity for the Stepwise Self-Assembly of M12L24 via M6L12 Metal–Organic Cages

Non-covalent interactions are important for directing protein folding across multiple intermediates and can even provide access to multiple stable structures with different properties and functions. Herein, we describe an approach for mimicking this behavior in the self-assembly of metal–organic cages. Two ligands, the bend angles of which are controlled by non-covalent interactions and one ligand lacking the above-mentioned interactions, were synthesized and used for self-assembly with Pd²⁺. As these weak interactions are easily broken, the bend angles have a controlled flexibility giving access to M₂( L1 )₄, M₆( L2 )₁₂, and M₁₂( L2 )₂₄ cages. By controlling the self-assembly conditions this process can be directed in a stepwise fashion. Additionally, the multiple endohedral hydrogen-bonding sites on the ligand were found to play a role in the binding and discrimination of neutral guests.     

Coinage metal complexes of N‐heterocyclic carbene bearing nitrile functionalization: Synthesis and photophysical properties

A new series of N‐heterocyclic carbene (NHC) ligand precursors ( 1 and 2 ) with their [Ag(I)(NHC)₂]PF₆ complexes ( 3 and 4 ) and [ClAu(I)(NHC)] complexes ( 5 and 6 ) are reported. Complexes 5 and 6 were synthesized via transmetalation reaction using either 3 or 4 and AuCl(SMe₂) as reactants, respectively. All the synthesized compounds were fully characterized using elemental analyses and Fourier transform infrared, ¹H NMR and ¹³C NMR spectroscopies. In the crystal structures of 3 , 5 and 6 , the Ag(I) and Au(I) ions are in a linear geometry. The entire structure of 3 is stabilized by significant π–π interactions, while the structures of 5 and 6 are stabilized with the presence of aurophilic interactions between the adjacent Au(I) ions as well as CH–π or π–π interactions. From photoluminescence studies, complexes 5 and 6 show dual‐emission characteristics. The higher‐energy fluorescence originates from ¹XLCT mixed with ¹MLCT, while the lower‐energy phosphorescence is ascribed to ³XLCT and ³MLCT with small contribution of ³ILCT, as evidenced by density functional theory (DFT) and time‐dependent DFT calculations of the modelled molecules.     

Metal-ligand coordination and antiradical activity of a trichromium(III) complex with the flavonoid naringenin

The trinuclear chromium(III) complex [Cr₃O(CH₃CO₂)₆(L)(H₂O)₂] (where L is the monoanion of the flavonoid naringenin) was synthesized and characterized. Density functional theory (DFT) calculations and quantum theory of atoms in molecules (QTAIM) analysis show that the flavonoid binds to Cr^III as an O,O-bidentate ligand via the 5-hydroxy and 4-oxo groups. Reactions with 2,2-diphenyl-1-picrylhydrazyl (DPPH) indicate that the antiradical activity of this flavonoid-metal complex is enhanced in comparison with uncoordinated naringenin.     

Anion Coreceptor Molecules. Linear Molecular Recognition in the Selective Binding of Dicarboxylate Substrates by Ditopic Polyammonium Macrocycles

Three macrocyclic hexaamines 1 , 2 , and 4 , and the acyclic tetraamine 5 and hexaamine 6 have been synthesized. The hexaamines 1 , 2 , and 4 are ditopic coreceptor molecules containing two triamine subunits which may bind anionic substrates when protonated. The stability constants of the complexes between the protonated forms of the macrocyclic polyamines and terminal dicarboxylates ^?O₂C?(CH₂)_m- CO₂^? as well as amino-acid and dipeptide dicarboxylates have been determined by pH-metric measurements. Around neutral pH, 1 and 2 give mainly complexes of the fully protonated species 1 ·6H⁺ and 2 ·6H⁺, whereas 4 yields predominantly complexes of 4 ·5H⁺ and 4 ·4H⁺. The stability sequences of the complexes formed indicate preferential binding of the dianionic substrates whose length is compatible with the separation of the triammonium binding subunits in the protonated receptor molecules 1 , 2 , and 4 . This selectivity pattern corresponds to a process of linear molecular recognition based on ditopic binding between the two ammonium subunits of the coreceptor and the terminal carboxylates of the substrate of complementary length. The complexes of the acyclic ligands 5 and 6 are much weaker and much less selective, indicating a marked macrocyclic effect on both stability and selectivity of binding, i.e. on recognition.     

Photochemical Reduction of Carbon Dioxide Catalyzed by a Ruthenium‐Substituted Polyoxometalate

A polyoxometalate of the Keggin structure substituted with Ru^III, ⁶Q₅[Ru^III(H₂O)SiW₁₁O₃₉] in which ⁶Q=(C₆H₁₃)₄N⁺, catalyzed the photoreduction of CO₂ to CO with tertiary amines, preferentially Et₃N, as reducing agents. A study of the coordination of CO₂ to ⁶Q₅[Ru^III(H₂O)SiW₁₁O₃₉] showed that 1) upon addition of CO₂ the UV/Vis spectrum changed, 2) a rhombic signal was obtained in the EPR spectrum (g_x=2.146, g_y=2.100, and g_z=1.935), and 3) the ¹³C NMR spectrum had a broadened peak of bound CO₂ at 105.78 ppm (Δ_1/2=122 Hz). It was concluded that CO₂ coordinates to the Ru^III active site in both the presence and absence of Et₃N to yield ⁶Q₅[Ru^III(CO₂)SiW₁₁O₃₉]. Electrochemical measurements showed the reduction of Ru^III to Ru^II in ⁶Q₅[Ru^III(CO₂)SiW₁₁O₃₉] at ?0.31 V versus SCE, but no such reduction was observed for ⁶Q₅[Ru^III(H₂O)SiW₁₁O₃₉]. DFT‐calculated geometries optimized at the M06/PC1//PBE/AUG‐PC1//PBE/PC1‐DF level of theory showed that CO₂ is preferably coordinated in a side‐on manner to Ru^III in the polyoxometalate through formation of a Ru? O bond, further stabilized by the interaction of the electrophilic carbon atom of CO₂ to an oxygen atom of the polyoxometalate. The end‐on CO₂ bonding to Ru^III is energetically less favorable but CO₂ is considerably bent, thus favoring nucleophilic attack at the carbon atom and thereby stabilizing the carbon sp² hybridization state. Formation of a O₂C–NMe₃ zwitterion, in turn, causes bending of CO₂ and enhances the carbon sp² hybridization. The synergetic effect of these two interactions stabilizes both Ru–O and C–N interactions and probably determines the promotional effect of an amine on the activation of CO₂ by [Ru^III(H₂O)SiW₁₁O₃₉]^5?. Electronic structure analysis showed that the polyoxometalate takes part in the activation of both CO₂ and Et₃N. A mechanistic pathway for photoreduction of CO₂ is suggested based on the experimental and computed results.     

Infrared Photodissociation Spectroscopic and Theoretical Study of [Co(CO2)n]+ Clusters

The mass-selected infrared photodissociation (IRPD) spectroscopy was utilized to investigate the interactions of cationic cobalt with carbon dioxide molecules. Quantum chemical calculations were performed on the [Co(CO₂)_n]⁺ clusters to identify the structures of the low-lying isomers and to assign the observed spectral features. All the [Co(CO₂)_n]⁺(n=2-6) clusters studied here show resonances near the CO₂ asymmetric stretch of free CO₂ molecule. Experimental and calculated results indicate that the CO₂ molecules are weakly bound to the Co⁺ cations in an end-on con guration via a charge-quadrupole electrostatic interaction. The present IRPD spectra of [Co(CO₂)_n]⁺ clusters have been compared to those of Ar-tagged species ([Co(CO₂)_n]⁺-Ar), which would provide insights into the tagging effect of rare gas on the weakly-bounded clusters.     

Designing GO Channels with High Selectivity for CO2/N2 Separation via Incorporating Metal Ions

Graphene oxide (GO) membranes holds great potential for high-performance CO₂ capture. Aiming at enhancing the CO₂ separation performance and structural stability of GO membranes, functionalizing GO channels with metal ions confers a promising strategy. In this study, we reported the fabrication of metal ion-incorporated GO membranes with remarkably improved CO₂/N₂ separation performance. The metal ions within GO channels contribute to facilitating CO₂ transport, decreasing N₂ solubility, hindering N₂ diffusion, and form multiple interactions with GO nanosheets. After introducing Mg²⁺ ions, the CO₂/N₂ separation factor of GO membrane is remarkably increased from 4 to 48.8 with the CO₂ permeance increases 1.5 times. Moreover, the separation performance of the GO-Mg²⁺ membranes shows an excellent long-term stability owing to the structural robustness. This study could provide insights into the regulation of the microstructure of metal ion-functionalized GO membranes for highly selective transport of specific molecules.     

Structural isomers of 2-(2,3 and 4-substituted-phenyl)-1,2-benzisoselenazol-3(2H)-one: A Theoretical Study

A series of 2-(2,3 and 4-substituted-phenyl)-1,2-benzisoselenazol-3(2H)-one molecules were theoretically investigated by the use of density functional theory (DFT) calculations at the B3LYP/6-311++G^∗∗ level of the theory. The substituents studied in this work are X = H; CH₃; NH₂; OH; OCH₃; F, Cl; Br; NO₂; CN; COCH₃; CO₂H; CO₂Me; SH; BH₂. We have selected these functional groups to be placed in the 2, 3 and 4 positions with relation to the benzisoselenazol moiety in order to show the effect of these structural modifications on the electronic properties of the molecules.