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Bakó I, Jicsinszky L, Pothoczki S. Systematic Study of Different Types of Interactions in α-, β- and γ-Cyclodextrin: Quantum Chemical Investigation. Molecules 2024; 29:2205. [PMID: 38792067 PMCID: PMC11124371 DOI: 10.3390/molecules29102205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/03/2024] [Accepted: 05/06/2024] [Indexed: 05/26/2024] Open
Abstract
In this work, comprehensive ab initio quantum chemical calculations using the DFT level of theory were performed to characterize the stabilization interactions (H-bonding and hyperconjugation effects) of two stable symmetrical conformations of α-, β-, and γ-cyclodextrins (CDs). For this purpose, we analyzed the electron density using "Atom in molecules" (AIM), "Natural Bond Orbital" (NBO), and energy decomposition method (CECA) in 3D and in Hilbert space. We also calculated the H-bond lengths and OH vibrational frequencies. In every investigated CD, the quantum chemical descriptors characterizing the strength of the interactions between the H-bonds of the primary OH (or hydroxymethyl) and secondary OH groups are examined by comparing the same quantity calculated for ethylene glycol, α-d-glucose (α-d-Glcp) and a water cluster as reference systems. By using these external standards, we can characterize more quantitatively the properties of these bonds (e.g., strength). We have demonstrated that bond critical points (BCP) of intra-unit H-bonds are absent in cyclodextrins, similar to α-d-Glcp and ethylene glycol. In contrast, the CECA analysis showed the existence of an exchange (bond-like) interaction between the interacting O…H atoms. Consequently, the exchange interaction refers to a chemical bond, namely the H-bond between two atoms, unlike BCP, which is not suitable for its detection.
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Affiliation(s)
- Imre Bakó
- HUN-REN Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, H-1117 Budapest, Hungary
| | - László Jicsinszky
- Dipartimento di Scienza e Tecnologia del Farmaco, University of Turin, Via P. Giuria, 9, 10125 Turin, Italy;
| | - Szilvia Pothoczki
- HUN-REN Wigner Research Centre for Physics, Konkoly Thege M. út 29-33, H-1121 Budapest, Hungary
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2
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Pantaleone S, Gho CI, Ferrero R, Brunella V, Corno M. Exploration of the Conformational Scenario for α-, β-, and γ-Cyclodextrins in Dry and Wet Conditions, from Monomers to Crystal Structures: A Quantum-Mechanical Study. Int J Mol Sci 2023; 24:16826. [PMID: 38069149 PMCID: PMC10706634 DOI: 10.3390/ijms242316826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 11/21/2023] [Accepted: 11/23/2023] [Indexed: 12/18/2023] Open
Abstract
Cyclodextrins (CDs) constitute a class of cyclic oligosaccharides that are well recognized and largely applied in the drug delivery field, thanks to their biocompatibility, low cost, and the possibility to be derivatized in order to tune and optimize the complexation/release of the specific drug. The conformational flexibility of these systems is one of their key properties and requires a cost-effective methodology to be studied by combining the accuracy of results with the possibility of exploring a large set of conformations. In the present paper, we have explored the conformational potential energy surface of the monomers and dimers of α-, β-, and γ-cyclodextrins (i.e., 6, 7, and 8 monomeric units, respectively) by means of fast but accurate semiempirical methods, which are then refined by state-of-the-art DFT functionals. Moreover, the crystal structure is considered for a more suitable comparison with the IR spectrum experimentally recorded. Calculations are carried out in the gas phase and in water environments, applying both implicit and explicit treatments. We show that the conformation of the studied molecules changes from the gas phase to the water, even if treated implicitly, thus modifying their complexation capability.
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Affiliation(s)
| | | | | | | | - Marta Corno
- Dipartimento di Chimica and Nanostructured Interfaces and Surfaces (NIS) Centre, Università degli Studi di Torino, Via P. Giuria 7, 10125 Torino, Italy; (S.P.); (C.I.G.); (R.F.); (V.B.)
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3
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Anconi CPA, Souza LCA. Multi-equilibrium approach to study cyclodextrins host–guest systems with GFN2-xTB quantum method: A case study of phosphorothioates included in β-cyclodextrin. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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4
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Muzaffar S, Imtiaz S, Ali SM. Demonstrating accuracy of the proposed protocol for structure elucidation of cyclodextrin inclusion complexes by validation using DFT studies. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128419] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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5
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Xu C, He N, Li Z, Chu Y, Ding CF. Exploring halide anion affinities to native cyclodextrins by mass spectrometry and molecular modelling. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2018; 24:269-278. [PMID: 29271243 DOI: 10.1177/1469066717748658] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The binding affinities of cyclodextrins complexation with chlorine (Cl-), bromine (Br-) and iodine (I-), were measured by mass spectrometric titrimetry, and the fitting of the binding constants was based on the concentration measurement of the cyclodextrin equilibrium. The binding constants (lg Ka) for α-, β- or γ-cyclodextrin with Cl- were 3.99, 4.03 and 4.11, respectively. The gas-phase binding affinity of halide anions for native cyclodextrins was probed by collision-induced dissociation. In collision-induced dissociation, the centre-of-mass frame energy results revealed that in the gas phase, for the same type of cyclodextrin, the stability of the complexes decreased in order: Cl > Br > I, and for the same halide anion, the binding stability of the complex with α-, β- or γ-cyclodextrin decreased in the order: γ-cyclodextrin >β-cyclodextrin > α-cyclodextrin. The density functional theory calculations showed that halide anion binding on the primary face had a lower energy than the secondary face and hydrogen bonding was the main driving force for complex formation. The higher stability of the γ-cyclodextrin complex with the Cl anion can be attributed to the higher charge density of the Cl anion and better flexibility of γ-cyclodextrin.
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Affiliation(s)
- Chongsheng Xu
- Department of Chemistry, Collaborative Innovation Center of Chemistry for Energy Material, Shanghai Key Laboratory of Molecular Catalysis & Innovative Materials, Fudan University, Shanghai, China
| | - Nan He
- Department of Chemistry, Collaborative Innovation Center of Chemistry for Energy Material, Shanghai Key Laboratory of Molecular Catalysis & Innovative Materials, Fudan University, Shanghai, China
| | - Zhenhua Li
- Department of Chemistry, Collaborative Innovation Center of Chemistry for Energy Material, Shanghai Key Laboratory of Molecular Catalysis & Innovative Materials, Fudan University, Shanghai, China
| | - Yanqiu Chu
- Department of Chemistry, Collaborative Innovation Center of Chemistry for Energy Material, Shanghai Key Laboratory of Molecular Catalysis & Innovative Materials, Fudan University, Shanghai, China
| | - Chuan-Fan Ding
- Department of Chemistry, Collaborative Innovation Center of Chemistry for Energy Material, Shanghai Key Laboratory of Molecular Catalysis & Innovative Materials, Fudan University, Shanghai, China
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6
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Investigation of 3D Contour Map and Intermolecular Interaction of Dopamine with β-Cyclodextrin and 2-Hydroxypropyl-β-cyclodextrin. J SOLUTION CHEM 2018. [DOI: 10.1007/s10953-018-0728-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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7
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Gamboa-Carballo JJ, Rana VK, Levalois-Grützmacher J, Gaspard S, Jáuregui-Haza U. Structures and stabilities of naturally occurring cyclodextrins: a theoretical study of symmetrical conformers. J Mol Model 2017; 23:318. [PMID: 29058088 DOI: 10.1007/s00894-017-3488-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 09/25/2017] [Indexed: 01/31/2023]
Abstract
A molecular modeling study of symmetrical conformers of α-, β-, and γ-cyclodextrins in the gas and aqueous phases was carried out using the M06-2X density functional method, with SMD employed as an implicit solvation model. Eight symmetrical conformers were found for each cyclodextrin. Values of geometrical parameters obtained from the modeling study were found to agree well with those obtained from X-ray diffraction structures. A vibrational analysis using harmonic frequencies was performed to determine thermodynamic quantities. The GIAO method was applied to determine proton and carbon-13 NMR chemical shifts, which were then compared with corresponding chemical shifts reported in the literature. Hydrogen-bonding patterns were analyzed using geometrical descriptors, and quantum chemical topology was explored by QTAIM analysis. The results of this study indicated that four of the eight conformers studied for each cyclodextrin are the most populated in aqueous solution. These results provide the foundations for future studies of host-guest complexes involving these cyclodextrins. Graphical abstract δΔGsolvation: variation of free Gibss energy of solvation.
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Affiliation(s)
- Juan José Gamboa-Carballo
- Instituto Superior de Tecnologías y Ciencias Aplicadas, Universidad de La Habana, Ave. Salvador Allende No. 1110, P.O. Box 6163, CP 10600, Plaza de la Revolución, La Habana, Cuba
| | - Vijay Kumar Rana
- Department of Chemistry and Applied Biosciences, Laboratory of Inorganic Chemistry, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, CH-8093, Zurich, Switzerland
| | - Joëlle Levalois-Grützmacher
- Department of Chemistry and Applied Biosciences, Laboratory of Inorganic Chemistry, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, CH-8093, Zurich, Switzerland
| | - Sarra Gaspard
- Laboratoire COVACHIM M2E, EA 3592 Université des Antilles, BP 250, 97157, Pointe-à-Pitrex CEDEX, Guadeloupe, French West Indies, France
| | - Ulises Jáuregui-Haza
- Instituto Superior de Tecnologías y Ciencias Aplicadas, Universidad de La Habana, Ave. Salvador Allende No. 1110, P.O. Box 6163, CP 10600, Plaza de la Revolución, La Habana, Cuba.
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8
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Formation of β-cyclodextrin complexes in an anhydrous environment. J Mol Model 2016; 22:207. [PMID: 27518085 PMCID: PMC4982878 DOI: 10.1007/s00894-016-3061-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 07/03/2016] [Indexed: 11/02/2022]
Abstract
The formation of inclusion complexes of β-cyclodextrin was studied at the melting temperature of guest compounds by differential scanning calorimetry. The complexes of long-chain n-alkanes, polyaromatics, and organic acids were investigated by calorimetry and IR spectroscopy. The complexation ratio of β-cyclodextrin was compared with results obtained in an aqueous environment. The stability and structure of inclusion complexes with various stoichiometries were estimated by quantum chemistry and molecular dynamics calculations. Comparison of experimental and theoretical results confirmed the possible formation of multiple inclusion complexes with guest molecules capable of forming hydrogen bonds. This finding gives new insight into the mechanism of formation of host-guest complexes and shows that hydrophobic interactions play a secondary role in this case. Graphical abstract The formation of complexes of β-cyclodextrin with selected n-alkanes, polyaromatics, and organic acids in an anhydrous environment is studied by differential scanning calorimetry, IR spectroscopy, and molecular modeling. The results obtained confirm the possible formation of multiple inclusion complexes with guest molecules capable of forming hydrogen bonds and give a new perspective on the mechanism of formation of host-guest complexes.
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9
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Ribeiro-Viana RM, Butera AP, Santos ES, Tischer CA, Alves RB, Pereira de Freitas R, Guimarães L, Varotti FP, Viana GHR, Nascimento CS. Revealing the Binding Process of New 3-Alkylpyridine Marine Alkaloid Analogue Antimalarials and the Heme Group: An Experimental and Theoretical Investigation. J Chem Inf Model 2016; 56:571-9. [DOI: 10.1021/acs.jcim.5b00742] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Renato M. Ribeiro-Viana
- Departamento
de Bioquímica e Biotecnologia, CCE, Universidade Estadual de Londrina, Londrina, PR 86057-970, Brazil
| | - Anna P. Butera
- Departamento
de Química, CCE, Universidade Estadual de Londrina, Londrina, PR 86057-970, Brazil
| | - Eliziane S. Santos
- Departamento
de Ciências Naturais (DCNAT), Universidade Federal de São João del-Rei, Campus Dom Bosco, São
João Del Rei, MG 36301-160, Brazil
| | - César A. Tischer
- Departamento
de Bioquímica e Biotecnologia, CCE, Universidade Estadual de Londrina, Londrina, PR 86057-970, Brazil
| | - Rosemeire B. Alves
- Departamento
de Química, Instituto de Ciências Exatas (ICEx), Universidade Federal de Minas Gerais (UFMG), Av. Pres, Antônio Carlos,
6627, Pampulha, Belo Horizonte, MG 31270-901, Brazil
| | - Rossimiriam Pereira de Freitas
- Departamento
de Química, Instituto de Ciências Exatas (ICEx), Universidade Federal de Minas Gerais (UFMG), Av. Pres, Antônio Carlos,
6627, Pampulha, Belo Horizonte, MG 31270-901, Brazil
| | - Luciana Guimarães
- Departamento
de Ciências Naturais (DCNAT), Universidade Federal de São João del-Rei, Campus Dom Bosco, São
João Del Rei, MG 36301-160, Brazil
| | - Fernando P. Varotti
- Núcleo
de Pesquisa em Química Biológica (NQBio), Universidade Federal de São João del-Rei, Campus Centro-Oeste, Divinópolis, MG 35501-296, Brazil
| | - Gustavo H. R. Viana
- Núcleo
de Pesquisa em Química Biológica (NQBio), Universidade Federal de São João del-Rei, Campus Centro-Oeste, Divinópolis, MG 35501-296, Brazil
| | - Clebio S. Nascimento
- Departamento
de Ciências Naturais (DCNAT), Universidade Federal de São João del-Rei, Campus Dom Bosco, São
João Del Rei, MG 36301-160, Brazil
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10
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Lopes JF, Nascimento CS, Anconi CPA, Santos HFD, Almeida WBD. Inclusion complex thermodynamics: The β-cyclodextrin and sertraline complex example. J Mol Graph Model 2015; 62:11-17. [PMID: 26340534 DOI: 10.1016/j.jmgm.2015.08.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 08/15/2015] [Accepted: 08/18/2015] [Indexed: 11/15/2022]
Abstract
Thermodynamic properties for β-cyclodextrin-Sertraline inclusion process was calculated at the density functional theory (DFT) level using the PBE0 functional with 6-31G(d,p), 6-31++G(d,p) and 6-311++G(2df,p) basis sets. Electron correlation was evaluated through Møller-Plesset second-order perturbation theory (MP2). The standard statistical thermodynamic approach was used to assess the entropic contribution to the Gibbs free energy value. According to our results, inclusion of hydration waters to describe the reactants and products in the complex formation reaction model is crucial in order to reproduce the experimental data and seems very coherent with basics thermodynamics yielding good agreement with experiment.
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Affiliation(s)
- Juliana Fedoce Lopes
- Laboratório de Química Computacional, LaQC, Instituto de Física e Química,Universidade Federal de Itajubá (UNIFEI), Av. BPS, 1303 Pinheirinho, Itajubá, MG 37500-903, Brazil
| | - Clebio S Nascimento
- Departamento de Ciências Naturais (DCNAT), Universidade Federal de São João Del-Rei, São João Del Rei, MG 36301-160, Brazil
| | - Cleber P A Anconi
- Laboratório de Química Fundamental (LQF), Departamento de Química, Universidade Federal de Lavras (UFLA), Lavras, MG 37200-000, Brazil
| | - Hélio F Dos Santos
- Núcleo de Estudos em Química Computacional (NEQC) - Departamento de Química, ICE, Universidade Federal de Juiz de Fora (UFJF), Campus Universitário, Martelos, Juiz de Fora, MG 36036-330, Brazil
| | - Wagner B De Almeida
- Laboratório de Química Computacional (LQC), Departamento de Química Inorgânica, Instituto de Química, Universidade Federal Fluminense, Campus do Valonguinho, Centro, Niterói, RJ CEP: 24020-141, Brazil.
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11
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Ma M, Su J, Sheng X, Su F, Li S, Xing P, Hao A. Rapid regio- and enantioselectivities and kinetic resolution of dl-lysine by an effective supramolecular system in water. J Mol Liq 2014. [DOI: 10.1016/j.molliq.2014.06.038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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12
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Yao Q, You B, Zhou S, Chen M, Wang Y, Li W. Inclusion complexes of cypermethrin and permethrin with monochlorotriazinyl-beta-cyclodextrin: a combined spectroscopy, TG/DSC and DFT study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 117:576-586. [PMID: 24103228 DOI: 10.1016/j.saa.2013.09.036] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2013] [Revised: 09/04/2013] [Accepted: 09/07/2013] [Indexed: 06/02/2023]
Abstract
The suitable size hydrophobic cavity and monochlorotriazinyl group as a reactive anchor make MCT-β-CD to be widely used in fabric finishing. In this paper, the inclusion complexes of monochlorotriazinyl-beta-cyclodextrin (MCT-β-CD) with cypermethrin (CYPERM) and permethrin (PERM) are synthesized and analyzed by TG/DSC, FT-IR and Raman spectroscopy. TG/DSC reveals that the decomposed temperatures of inclusion complexes are lower by 25-30 °C than that of physical mixtures. DFT calculations in conjunction with FT-IR and Raman spectral analyses are used to study the structures of MCT-β-CD and their inclusion complexes. Four isomers of trisubstituted MCT-β-CD are designed and DFT calculations reveal that 1,3,5-trisubstituted MCT-β-CD has the lowest energy and can be considered as main component of MCT-β-CD. The ground-state geometries, vibrational wavenumbers, IR and Raman intensities of MCT-β-CD and their inclusion complexes were calculated at B3LYP/6-31G (d) level of theory. Upon examining the optimized geometry of inclusion complex, we find that the CYPERM and PERM are inserted into the toroid of MCT-β-CD from the larger opening. The band at 1646 cm(-1) in IR and at 1668 cm(-1) in Raman spectrum reveals that monochloroazinyl group of MCT-β-CD exists in ketone form but not in anion form. The noticeable IR and Raman shift of phenyl reveals that these two benzene rings of CYPERM and PERM stays inside the cavity of MCT-β-CD and has weak interaction with MCT-β-CD. This spectroscopy conclusion is consistent with theoretical predicted structure.
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Affiliation(s)
- Qi Yao
- School of Chemistry and Chemical engineering, Wuhan Textile University, 430073 Wuhan, China
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13
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Piras L, Theodossiou TA, Manouilidou MD, Lazarou YG, Sortino S, Yannakopoulou K. S-nitroso-β-cyclodextrins as new bimodal carriers: preparation, detailed characterization, nitric-oxide release, and molecular encapsulation. Chem Asian J 2013; 8:2768-78. [PMID: 23894118 DOI: 10.1002/asia.201300543] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Linda Piras
- Institute of Advanced Materials, Physicochemical Processes, Nanotechnology and Microsystems, Terma Patr. Gregoriou, Aghia Paraskevi Attikis, 15310 (Greece), Fax: (+30) 210-6511766
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14
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Gámez F, Hurtado P, Hortal AR, Martínez-Haya B, Berden G, Oomens J. Cations in a Molecular Funnel: Vibrational Spectroscopy of Isolated Cyclodextrin Complexes with Alkali Metals. Chemphyschem 2012; 14:400-7. [DOI: 10.1002/cphc.201200810] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Indexed: 11/10/2022]
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15
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Zhang H, Tan T, Feng W, van der Spoel D. Molecular Recognition in Different Environments: β-Cyclodextrin Dimer Formation in Organic Solvents. J Phys Chem B 2012; 116:12684-93. [DOI: 10.1021/jp308416p] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Haiyang Zhang
- Department of Biochemical Engineering,
Beijing Key Laboratory of Bioprocess, Beijing University of Chemical Technology, Box 53, 100029 Beijing, China
- Department of Cell and Molecular
Biology, Science for Life Laboratory, Uppsala University, Husargatan 3, Box 596, SE-751 24 Uppsala, Sweden
| | - Tianwei Tan
- Department of Biochemical Engineering,
Beijing Key Laboratory of Bioprocess, Beijing University of Chemical Technology, Box 53, 100029 Beijing, China
| | - Wei Feng
- Department of Biochemical Engineering,
Beijing Key Laboratory of Bioprocess, Beijing University of Chemical Technology, Box 53, 100029 Beijing, China
| | - David van der Spoel
- Department of Cell and Molecular
Biology, Science for Life Laboratory, Uppsala University, Husargatan 3, Box 596, SE-751 24 Uppsala, Sweden
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16
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Bao X, Tao P, Villamena FA, Hadad CM. Spin trapping of hydroperoxyl radical by a cyclic nitrone conjugated to β-cyclodextrin: a computational study. Theor Chem Acc 2012; 131. [PMID: 23585725 DOI: 10.1007/s00214-012-1248-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Spin trapping of hydroperoxyl radical (HOO.) by the amide-linked conjugate of 5-carbamoyl-5-methyl-1-pyrroline N-oxide (AMPO) to β-cyclodextrin (β-CD) was studied computationally using a two-layered ONIOM method. From a conformational perspective, the "internal" conformation of 5R-β-CD-AMPO is more favored than the "external" conformation in which the nitrone is located outside of the cavity of the β-CD. When the HOO. addition product is formed, the most stable isomer has the nitroxyl (N1-O1) moiety pointing inside the cavity of the β-CD. Thus, this "internal" conformation might protect the N1-O1 moiety of the resulting spin adduct from access by reducing agents, thereby improving the lifetime of the radical adduct. The computed energetic barrier for HOO. addition to the 5R-β-CD-AMPO is 8.7 kcal/mol, which is marginally smaller than spin trapping by the non-conjugated AMPO (that is, without the β-CD). To optimize the reactivity of the β-CD-AMPO conjugate, the effect of a spacer unit between the AMPO segment and the β-CD moiety with varying methylene units, (CH2) n (n = 1, 2, 3), on the energetics of HOO. addition was evaluated. The structure with only one methylene spacer (n = 1) appears to be optimal as determined by the smaller activation barrier (6.2 kcal/mol) for HOO. addition to the nitrone moiety. Compared with very time-consuming quantum mechanical methods, the ONIOM method appears to offer significant advantages for evaluation of the best β-CD-AMPO conjugate for trapping of such reactive oxygen species and providing for the rational design of novel nitrones as spin traps.
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Affiliation(s)
- Xiaoguang Bao
- Department of Chemistry, Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA
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17
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Li Z, Couzijn EPA, Zhang X. Intrinsic Properties of α-Cyclodextrin Complexes with Benzoate Derivatives in the Gas Phase: An Experimental and Theoretical Study. J Phys Chem B 2012; 116:943-50. [DOI: 10.1021/jp210329a] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zhongshu Li
- Laboratorium für Organische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10, CH-8093, Switzerland
| | - Erik P. A. Couzijn
- Laboratorium für Organische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10, CH-8093, Switzerland
| | - Xiangyang Zhang
- Laboratorium für Organische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10, CH-8093, Switzerland
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18
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Li Z, Couzijn EPA, Zhang X. A quantitative study of intrinsic non-covalent interactions within complexes of α-cyclodextrin and benzoate derivatives. Chem Commun (Camb) 2012; 48:9864-6. [DOI: 10.1039/c2cc34728h] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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19
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Granero-García R, Lahoz FJ, Paulmann C, Saouane S, Fabbiani FPA. A novel hydrate of α-cyclodextrin crystallised under high-pressure conditions. CrystEngComm 2012. [DOI: 10.1039/c2ce26362a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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20
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Transition metal complexes enslaved in the supercages of zeolite-Y: DFT investigation and catalytic significance. J INCL PHENOM MACRO 2011. [DOI: 10.1007/s10847-011-0090-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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21
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Anconi CP, da Silva Delgado L, Alves dos Reis JB, De Almeida WB, Costa LAS, Dos Santos HF. Inclusion complexes of α-cyclodextrin and the cisplatin analogues oxaliplatin, carboplatin and nedaplatin: A theoretical approach. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.09.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Stachowicz A, Styrcz A, Korchowiec J, Modaressi A, Rogalski M. DFT studies of cation binding by β-cyclodextrin. Theor Chem Acc 2011. [DOI: 10.1007/s00214-011-1014-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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23
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Barraza LF, Alderete JB, Jiménez VA, Gavín JA. Diffusion coefficients of first-generation polyamidoamine dendrimer and its β-cyclodextrin conjugate in aqueous solution by means of molecular dynamics simulations. MONATSHEFTE FUR CHEMIE 2011. [DOI: 10.1007/s00706-011-0555-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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Host–guest complex of cypermethrin with β-cyclodextrin: A spectroscopy and theoretical investigation. J Mol Struct 2011. [DOI: 10.1016/j.molstruc.2011.01.053] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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25
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Li W, Lu B, Sheng A, Yang F, Wang Z. Spectroscopic and theoretical study on inclusion complexation of beta-cyclodextrin with permethrin. J Mol Struct 2010. [DOI: 10.1016/j.molstruc.2010.08.008] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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26
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Density functional calculations on meloxicam–β-cyclodextrin inclusion complexes. Int J Pharm 2009; 381:146-52. [DOI: 10.1016/j.ijpharm.2009.05.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2008] [Revised: 04/22/2009] [Accepted: 05/06/2009] [Indexed: 11/19/2022]
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27
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Pinjari RV, Khedkar JK, Gejji SP. Cavity diameter and height of cyclodextrins and cucurbit[n]urils from the molecular electrostatic potential topography. J INCL PHENOM MACRO 2009. [DOI: 10.1007/s10847-009-9657-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Anconi CPA, Nascimento CS, De Almeida WB, Dos Santos HF. Structure and Stability of (α-CD)3 Aggregate and OEG@(α-CD)3 Pseudorotaxane in Aqueous Solution: A Molecular Dynamics Study. J Phys Chem B 2009; 113:9762-9. [DOI: 10.1021/jp903166e] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Cleber P. A. Anconi
- Núcleo de Estudos em Química Computacional (NEQC), Departamento de Química, ICE, Universidade Federal de Juiz de Fora (UFJF), Campus Universitário, Martelos, Juiz de Fora, MG 36036-330, Brazil, and Laboratório de Química Computacional e Modelagem Molecular (LQC-MM), Departamento de Química, ICEx, Universidade Federal de Minas Gerais (UFMG), Campus Universitário, Pampulha, Belo Horizonte, MG 31270-901, Brazil
| | - Clebio S. Nascimento
- Núcleo de Estudos em Química Computacional (NEQC), Departamento de Química, ICE, Universidade Federal de Juiz de Fora (UFJF), Campus Universitário, Martelos, Juiz de Fora, MG 36036-330, Brazil, and Laboratório de Química Computacional e Modelagem Molecular (LQC-MM), Departamento de Química, ICEx, Universidade Federal de Minas Gerais (UFMG), Campus Universitário, Pampulha, Belo Horizonte, MG 31270-901, Brazil
| | - Wagner B. De Almeida
- Núcleo de Estudos em Química Computacional (NEQC), Departamento de Química, ICE, Universidade Federal de Juiz de Fora (UFJF), Campus Universitário, Martelos, Juiz de Fora, MG 36036-330, Brazil, and Laboratório de Química Computacional e Modelagem Molecular (LQC-MM), Departamento de Química, ICEx, Universidade Federal de Minas Gerais (UFMG), Campus Universitário, Pampulha, Belo Horizonte, MG 31270-901, Brazil
| | - Hélio F. Dos Santos
- Núcleo de Estudos em Química Computacional (NEQC), Departamento de Química, ICE, Universidade Federal de Juiz de Fora (UFJF), Campus Universitário, Martelos, Juiz de Fora, MG 36036-330, Brazil, and Laboratório de Química Computacional e Modelagem Molecular (LQC-MM), Departamento de Química, ICEx, Universidade Federal de Minas Gerais (UFMG), Campus Universitário, Pampulha, Belo Horizonte, MG 31270-901, Brazil
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Su JW, Burnette RR. First principles investigation of noncovalent complexation: a [2.2.2]-cryptand ion-binding selectivity study. Chemphyschem 2008; 9:1989-96. [PMID: 18792032 DOI: 10.1002/cphc.200800376] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A first principles methodology, aimed at understanding the roles of molecular conformation and energetics in host-guest binding interactions, is developed and tested on a system that pushes the practical limits of ab initio methods. The binding behavior between the [2.2.2]-cryptand host (4,7,13,16,21,24-hexaoxa-1,10-diaza-bicyclo[8.8.8]hexacosane) and alkali metal cations (Li(+), Na(+), and K(+)) in gas, water, methanol, and acetonitrile is characterized. Hartree-Fock and density functional theory methods are used in concert with crystallographic information to identify gas phase, energy-minimized conformations. Gas phase free energies of binding, with vibrational contributions, are compared to solution-state binding constants through relative binding selectivity analysis. Calculated relative binding free energies qualitatively correlated with solution state experiments only after gas phase metal desolvation is considered. The B3LYP exchange-correlation functional improves theoretical correlations with experimental relative binding free energies. The relevance of gas phase calculations towards understanding binding in condensed phases is discussed. Natural bond orbital methods highlights previously unidentified intramolecular and intermolecular M(+)(222) chemistries, such as an intramolecular n'(O)-->sigma*(CH) hydrogen bond.
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Affiliation(s)
- Joe W Su
- School of Pharmacy, University of Wisconsin, 777 Highland Ave., Madison, WI 53705, USA
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