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Yanes-Rodríguez R, Prosmiti R. Analysing the stability of He-filled hydrates: how many He atoms fit in the sII crystal? Phys Chem Chem Phys 2024; 26:2519-2528. [PMID: 38170811 DOI: 10.1039/d3cp05410a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Clathrate hydrates have the ability to encapsulate atoms and molecules within their cavities, and thus they could be potentially large storage capacity materials. The present work studies the multiple cage occupancy effects in the recently discovered He@sII crystal. On the basis of previous theoretical and experimental findings, the stability of He(1/1)@sII, He(1/4)@sII and He(2/4)@sII crystals was analysed in terms of structural, mechanical and energetic properties. For this purpose, first-principles DFT/DFT-D computations were performed by using both semi-local and non-local functionals, not only to elucidate which configuration is the most energetically favoured, but also to scrutinize the relevance of the long-range dispersion interactions in these kinds of compounds. We have encountered that dispersion interactions play a fundamental role in describing the underlying interactions, and different tendencies were observed depending on the choice of the functional. We found that PW86PBE-XDM shows the best performance, while the non-local functionals tested here were not able to correctly account for them. The present results reveal that the most stable configuration is the one presenting singly occupied D cages and tetrahedrally occupied H cages (He(1/4)@sII) in line with the experimental observation.
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Affiliation(s)
| | - Rita Prosmiti
- Institute of Fundamental Physics (IFF-CSIC), CSIC, Serrano 123, 28006 Madrid, Spain.
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2
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Sarkar M, Hey-Hawkins E, Boomishankar R. Encapsulation Studies on closo-Dicarbadodecaborane Isomers in Neutral Tetrahedral Palladium(II) Cages. Inorg Chem 2023; 62:4035-4042. [PMID: 36857772 DOI: 10.1021/acs.inorgchem.2c04207] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
The encapsulation of icosahedral closo-dicarbadodecaborane (o-, m-, and p-carboranes, Cb) as guest molecules at the intrinsic cavities of the three isostructural tetrahedral cages [{Pd3(NiPr)3PO}4(Cl-AN)6] (1), [{Pd3(NiPr)3PO}4(Br-AN)6] (2), and [{Pd3(NiPr)3PO}4(H-AN)6] (3) was studied. The formation of definite host-guest assemblies was probed with mass spectrometry, IR, and NMR spectral analysis. 2D DOSY 1H NMR of the Cb⊂Cage systems showed similar diffusion coefficient (D) values for the host and guest species, signifying the encapsulation of these guests inside the cage assemblies. The hydrodynamic radius (RH) derived from the D values of the host and guest species further confirmed the encapsulation of the Cb isomers at the cage pockets. The single-molecule energy optimization of the host-guest assemblies indicated the preferential binding of o-Cb as a guest inside the cages (1-3). The stabilization of these Cb guests inside these cages was further attributed to various possible nonclassical C-H···X-type interactions.
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Affiliation(s)
- Meghamala Sarkar
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
| | - Evamarie Hey-Hawkins
- Institut für Anorganische Chemie, Fakultät für Chemie und Mineralogie, Universität Leipzig, Johannisallee 29, 04103 Leipzig, Germany
| | - Ramamoorthy Boomishankar
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India.,Centre for Energy Science, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
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Sarkar M, Boomishankar R. Mapping the Assembly of Neutral Tetrahedral Cages Tethered by Oximido Linkers and Their Guest Encapsulation Studies. Inorg Chem 2023; 62:1855-1863. [PMID: 35623320 DOI: 10.1021/acs.inorgchem.2c01178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A primary criterion for the design of polyhedral metal-organic cages is the requirement of geometrically matched pairs of metal ions and ligand moieties. However, understanding the pathway it takes to reach the final polyhedral structure can provide more insights into the self-assembly process and improved design strategies. In this regard, we report two neutral tetrahedral cages with the formulas {[Pd3(NiPr)3PO]4(L1)6} (1-TD) and {[Pd3(NiPr)3PO]4(L2)6} (2-TD) starting from the acetate-bridged cluster {[Pd3(NiPr)3PO]2(OAc)2(OH)}2·2(CH3)2SO (HEXA-Pd) and the respective oxamide precursors (L1H2: [C2(NH2)2O2]) and (L2H2: (C2(NHMe)2O2]). When subtle variations in the reaction conditions were made, two new tetrameric Pd12 assemblies, {[Pd3(NiPr)3PO]4(L1)2(OAc)4(OMe)4} (1-TM) and {[Pd3(NiPr)3PO]4(L2)2(OAc)4(OMe)4} (2-TM), were obtained from the same precursors. Detailed investigations using NMR, mass spectrometry, X-ray crystallography, and computational studies indicate that the macrocyclic complexes 1-TM and 2-TM are the reaction intermediates involved in the formation of the tetrahedral cages 1-TD and 2-TD, respectively. Moreover, the tetrahedral cages 1-TD and 2-TD exhibited intrinsic cavities of volume ∼85 Å3. Guest encapsulation studies revealed that the cage 1-TD can encapsulate a wide range of guest molecules such as CH2Cl2, CHCl3, CCl4, C6H6, and C6H5F. Interestingly, 1-TD was shown to exhibit a preferential binding of C6H5F and C6H6 over other halogenated guest molecules, as determined from NMR titrations and computational studies.
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Affiliation(s)
- Meghamala Sarkar
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
| | - Ramamoorthy Boomishankar
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India.,Centre for Energy Science, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
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Yadav A, Sarkar M, Subrahmanyam S, Chaudhary A, Hey-Hawkins E, Boomishankar R. Anilate Tethered Neutral Tetrahedral Pd(II) Cages Exhibiting Selective Encapsulation of Xylenes and Mesitylene. Chemistry 2020; 26:4209-4213. [PMID: 31916272 DOI: 10.1002/chem.201905852] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Indexed: 01/25/2023]
Abstract
The design of porous materials for the recognition of multiple hydrocarbons is highly desirable for the energy-efficient separation and recognition of chemical feedstock. Herein, three new iso-structural porous discrete metal-organic cages of formula {[Pd3 (NiPr)3 PO]4 (R-AN)6 } (R-AN=anilate linkers) for the selective recognition of substituted aromatic hydrocarbons are reported. The tetrahedral cages 1, 2, and 3 containing anilate, chloranilate, and bromanilate linkers exhibited selective encapsulation of mesitylene, o-xylene, and p-xylene, respectively, over other analogous aromatic hydrocarbons. These selective encapsulations were driven by the variations in the portal diameters present at each of these cages and their interactions with the hydrocarbon guests. These observations are supported by mass spectrometry, NMR studies, and theoretical binding-energy calculations.
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Affiliation(s)
- Ashok Yadav
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pune, 411008, India
| | - Meghamala Sarkar
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pune, 411008, India
| | - Sappati Subrahmanyam
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pune, 411008, India
| | - Atul Chaudhary
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pune, 411008, India
| | - Evamarie Hey-Hawkins
- Institut für Anorganische Chemie, Fakultät für Chemie und Mineralogie, Universität Leipzig, 04103, Leipzig, Germany
| | - Ramamoorthy Boomishankar
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pune, 411008, India.,Centre of Energy Science, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pune, 411008, India
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Affiliation(s)
- Surinder Pal Kaur
- Department of Chemistry, Indian Institute of Technology Roorkee, Uttarakhand, India-247667
| | - C. N. Ramachandran
- Department of Chemistry, Indian Institute of Technology Roorkee, Uttarakhand, India-247667
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Effect of multiple and adjacent cage occupancies on host-guest interaction and NMR chemical shifts in gas hydrates. COMPUT THEOR CHEM 2016. [DOI: 10.1016/j.comptc.2016.07.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Gurav ND, Gejji SP, Bartolotti LJ, Pathak RK. Encaged molecules in external electric fields: A molecular "tug-of-war". J Chem Phys 2016; 145:074302. [PMID: 27544100 DOI: 10.1063/1.4960608] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Response of polar molecules CH3OH and H2O2 and a non-polar molecule, CO2, as "guests" encapsulated in the dodecahedral water cage (H2O)20 "host," to an external, perturbative electric field is investigated theoretically. We employ the hybrid density-functionals M06-2X and ωB97X-D incorporating the effects of damped dispersion, in conjunction with the maug-cc-pVTZ basis set, amenable for a hydrogen bonding description. While the host cluster (cage) tends to confine the embedded guest molecule through cooperative hydrogen bonding, the applied electric field tends to rupture the cluster-composite by stretching it; these two competitive effects leading to a molecular "tug-of-war." The composite remains stable up to a maximal sustainable threshold electric field, beyond which, concomitant with the vanishing of the HOMO-LUMO gap, the field wins over and the cluster breaks down. The electric-field effects are gauged in terms of the changes in the molecular geometry of the confined species, interaction energy, molecular electrostatic potential surfaces, and frequency shifts of characteristic normal vibrations in the IR regime. Interestingly, beyond the characteristic threshold electric field, the labile, distorted host cluster fragmentizes, and the guest molecule still tethered to a remnant fragment, an effect attributed to the underlying hydrogen-bonded networks.
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Affiliation(s)
- Nalini D Gurav
- Department of Physics, Savitribai Phule Pune University, Pune, Maharashtra 411007, India
| | - Shridhar P Gejji
- Department of Chemistry, Savitribai Phule Pune University, Pune, Maharashtra 411007, India
| | - Libero J Bartolotti
- Department of Physical and Computational Chemistry, East Carolina University, Greenville, North Carolina 27858, USA
| | - Rajeev K Pathak
- Department of Physics, Savitribai Phule Pune University, Pune, Maharashtra 411007, India
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Liu J, Liu H, Xu J, Chen G, Zhang J, Wang S. Structure and stability of multiply occupied methane clathrate hydrates. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.08.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Gupta AK, Yadav A, Srivastava AK, Ramya KR, Paithankar H, Nandi S, Chugh J, Boomishankar R. A Neutral Cluster Cage with a Tetrahedral [Pd12IIL6] Framework: Crystal Structures and Host–Guest Studies. Inorg Chem 2015; 54:3196-202. [DOI: 10.1021/ic502798r] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Arvind K. Gupta
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
| | - Ashok Yadav
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
| | - Anant Kumar Srivastava
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
| | - Kormathmadam Raghupathy Ramya
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
| | - Harshad Paithankar
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
| | - Shyamapada Nandi
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
| | - Jeetender Chugh
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
| | - Ramamoorthy Boomishankar
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
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Ramya K, Kumar R, Venkatnathan A. Energy and spectral characteristics of hydrogen occupied pure and tetrahydrofuran doped water cages. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.04.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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