1
|
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.
Collapse
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
| |
Collapse
|
2
|
Lai Z, Shen M, Shen Y, Ye YX, Zhu F, Xu J, Ouyang G. Hydrogen bond networks in gas-phase complex anions. RSC Adv 2022; 12:29137-29142. [PMID: 36320744 PMCID: PMC9558071 DOI: 10.1039/d2ra05029c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 10/02/2022] [Indexed: 11/05/2022] Open
Abstract
Hydrogen bond networks (HBNs) have piqued the interest of the scientific community due to their crucial roles in nature. However, HBNs that are isolated from complicated backgrounds for unraveling their characteristics are still scarce. Herein, we propose that HBNs exist in complex anions formed between α-cyclodextrin (α-CD) and four benzoic acids (RBAs) in the gas phase. The complex anions are facilely extracted from solutions via the electrospray ionization technique, and subsequently activated through collision for the investigation of their transition dynamics. It is revealed that the generation of deprotonated α-CD and neutral RBAs is the unexpected dominant dissociation pathway for all the four complex anions, and the complex anions formed from more acidic RBAs exhibit higher stabilities. These dissociation results are successfully explained by the cooperative stretching dynamics of the proposed HBNs that are formed involving the intramolecular HBN of α-CD and the intermolecular hydrogen bonds (HBs) between α-CD and RBAs. Furthermore, the rarely observed low barrier HBs (LBHBs) are suggested to be present in the HBNs. It is believed that the present complex anions can serve as a facilely accessible and informative model for studying HBNs in the future. Hydrogen bond networks and low barrier hydrogen bonds are demonstrated in the complex anions formed between α-cyclodextrin and benzoic acids.![]()
Collapse
Affiliation(s)
- Zhisheng Lai
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen UniversityGuangzhou510006China
| | - Minhui Shen
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen UniversityGuangzhou510006China
| | - Yong Shen
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen UniversityGuangzhou510006China
| | - Yu-Xin Ye
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen UniversityGuangzhou510006China
| | - Fang Zhu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen UniversityGuangzhou510006China
| | - Jianqiao Xu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen UniversityGuangzhou510006China
| | - Gangfeng Ouyang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen UniversityGuangzhou510006China,College of Chemistry, Center of Advanced Analysis and Gene Sequencing, Zhengzhou UniversityZhengzhou450001China,Guangdong Provincial Key Laboratory of Emergency Testing for Dangerous Chemicals, Guangdong Institute of Analysis (China National Analytical Center Guangzhou), Guangdong Academy of SciencesGuangzhou510070China
| |
Collapse
|
3
|
Rabus JM, Pellegrinelli RP, Khodr AHA, Bythell BJ, Rizzo TR, Carrascosa E. Unravelling the structures of sodiated β-cyclodextrin and its fragments. Phys Chem Chem Phys 2021; 23:13714-13723. [PMID: 34128027 PMCID: PMC8220536 DOI: 10.1039/d1cp01058a] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 06/05/2021] [Indexed: 12/29/2022]
Abstract
We present cryogenic infrared spectra of sodiated β-cyclodextrin [β-CD + Na]+, a common cyclic oligosaccharide, and its main dissociation products upon collision-induced dissociation (CID). We characterize the parent ions using high-resolution ion mobility spectrometry and cryogenic infrared action spectroscopy, while the fragments are characterized by their mass and cryogenic infrared spectra. We observe sodium-cationized fragments that differ in mass by 162 u, corresponding to Bn/Zm ions. For the m/z 347 product ion, electronic structure calculations are consistent with formation of the lowest energy 2-ketone B2 ion structure. For the m/z 509 product ion, both the calculated 2-ketone B3 and the Z3 structures show similarities with the experimental spectrum. The theoretical structure most consistent with the spectrum of the m/z 671 ions is a slightly higher energy 2-ketone B4 structure. Overall, the data suggest a consistent formation mechanism for all the observed fragments.
Collapse
Affiliation(s)
- Jordan M Rabus
- Department of Chemistry and Biochemistry, Ohio University, 391 Clippinger Laboratories, Athens, Ohio 45701, USA
| | - Robert P Pellegrinelli
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland.
| | - Ali Hassan Abi Khodr
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland.
| | - Benjamin J Bythell
- Department of Chemistry and Biochemistry, Ohio University, 391 Clippinger Laboratories, Athens, Ohio 45701, USA
| | - Thomas R Rizzo
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland.
| | - Eduardo Carrascosa
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland.
| |
Collapse
|
4
|
Yan X, Wang Y, Meng T, Yan H. Computational Insights Into the Influence of Substitution Groups on the Inclusion Complexation of β-Cyclodextrin. Front Chem 2021; 9:668400. [PMID: 34095084 PMCID: PMC8176092 DOI: 10.3389/fchem.2021.668400] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 05/03/2021] [Indexed: 11/21/2022] Open
Abstract
Cyclodextrins (CDs) and their derivatives have good prospects in soil remediation application due to their ability to enhance the stability and solubility of low water-soluble compounds by inclusion performance. To investigate the effect of different structural properties of cyclodextrin and its derivatives on the inclusion complexation, molecular dynamic (MD) simulations were performed on the inclusion complexes formed by three kinds of CDs with polycyclic aromatic hydrocarbons (PAHs). Based on neutral β-CD, the other two CDs were modified by introducing substitutional groups, including 2-hydroxypropyl and sulfonated butyl (SBE) functional groups in the ring structure, called HP-CD and SBE-CD. MD results show that PAH can merely enter into the cavity of SBE–β-CD from its wide rim. The substitutional groups significantly affect the structure of CDs, which may also cause the flipping of the glucose units. However, the substitutional groups can also enlarge the volume of the hydrophobic cavity, resulting in a tight combination with the guest molecules.
Collapse
Affiliation(s)
- Xianghua Yan
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, China.,School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, China
| | - Yue Wang
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, China
| | - Tong Meng
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, China
| | - Hui Yan
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, China
| |
Collapse
|
5
|
Dossmann H, Fontaine L, Weisgerber T, Bonnet V, Monflier E, Ponchel A, Przybylski C. First Steps to Rationalize Host-Guest Interaction between α-, β-, and γ-Cyclodextrin and Divalent First-Row Transition and Post-transition Metals (Subgroups VIIB, VIIIB, and IIB). Inorg Chem 2021; 60:930-943. [PMID: 33375780 DOI: 10.1021/acs.inorgchem.0c03052] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cyclodextrins (CDs) are cyclic oligosaccharides mainly composed of six, seven, and eight glucose units, so-called α-, β-, and γ-CDs, respectively. They own a very particular molecular structure exhibiting hydrophilic features thanks to primary and secondary rims and delimiting a hydrophobic internal cavity. The latter can encapsulate organic compounds, but the former can form supramolecular complexes by hydrogen-bonding or electrostatic interactions. CDs have been used in catalytic processes to increase mass transfer in aqueous-organic two-phase systems or to prepare catalysts. In the last case, interaction between CDs and metal salts was considered to be a key point in obtaining highly active catalysts. Up to now, no work was reported on the investigation of factors affecting the binding of metal to CD. In the study herein, we present the favorable combination of electrospray ionization coupled to mass spectrometry [ESI-MS(/MS)] and density functional theory molecular modeling [B3LYP/Def2-SV(P)] to delineate some determinants governing the coordination of first-row divalent transition metals (Mn2+, Co2+, Ni2+, Cu2+, and Fe2+) and one post-transition metal (Zn2+) with α-, β-, and γ-CDs. A large set of features concerning the metal itself (ionic radius, electron configuration, and spin state) as well as the complexes formed (the most stable conformer, relative abundance in MS, CE50 value in MS/MS, binding energy, effective coordination number, average bond lengths, binding site localization, bond dissociation energies, and natural bond orbital distribution) were screened. Taking into account all of these properties, various selectivity rankings have been delineated, portraying differential association/dissociation behaviors. Nonetheless, unique 3D topologies for each CD-metal complex were emphasized. The combination of these approaches brings a stone for building a compendium of molecular features to serve as a suitable descriptor or predictor for a better first round rationalization of catalytic activities.
Collapse
Affiliation(s)
- Héloïse Dossmann
- Institut Parisien de Chimie Moléculaire, Sorbonne Université, CNRS, F-75005 Paris, France
| | - Lucas Fontaine
- Laboratoire de Glycochimie, des Antimicrobiens et des Agroressources, Université de Picardie Jules Verne, CNRS, UMR 7378, 80039 Amiens, France
| | - Teddy Weisgerber
- Laboratoire de Glycochimie, des Antimicrobiens et des Agroressources, Université de Picardie Jules Verne, CNRS, UMR 7378, 80039 Amiens, France
| | - Véronique Bonnet
- Laboratoire de Glycochimie, des Antimicrobiens et des Agroressources, Université de Picardie Jules Verne, CNRS, UMR 7378, 80039 Amiens, France
| | - Eric Monflier
- Unité de Catalyse et Chimie du Solide, Université Artois, CNRS, Centrale Lille, Université Lille, UMR 8181, F-62300 Lens, France
| | - Anne Ponchel
- Unité de Catalyse et Chimie du Solide, Université Artois, CNRS, Centrale Lille, Université Lille, UMR 8181, F-62300 Lens, France
| | - Cédric Przybylski
- Institut Parisien de Chimie Moléculaire, Sorbonne Université, CNRS, F-75005 Paris, France
| |
Collapse
|
6
|
Melnikova DL, Badrieva ZF, Kostin MA, Maller C, Stas M, Buczek A, Broda MA, Kupka T, Kelterer AM, Tolstoy PM, Skirda VD. On Complex Formation between 5-Fluorouracil and β-Cyclodextrin in Solution and in the Solid State: IR Markers and Detection of Short-Lived Complexes by Diffusion NMR. Molecules 2020; 25:E5706. [PMID: 33287255 PMCID: PMC7731325 DOI: 10.3390/molecules25235706] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 11/27/2020] [Accepted: 11/30/2020] [Indexed: 11/16/2022] Open
Abstract
In this work, the nuclear magnetic resonance (NMR) and IR spectroscopic markers of the complexation between 5-fluorouracil (5-FU) and β-cyclodextrin (β-CD) in solid state and in aqueous solution are investigated. In the attenuated total reflectance(ATR) spectra of 5-FU/β-CD products obtained by physical mixing, kneading and co-precipitation, we have identified the two most promising marker bands that could be used to detect complex formations: the C=O and C-F stretching bands of 5-FU that experience a blue shift by ca. 8 and 2 cm-1 upon complexation. The aqueous solutions were studied by NMR spectroscopy. As routine NMR spectra did not show any signs of complexation, we have analyzed the diffusion attenuation of spin-echo signals and the dependence of the population factor of slowly diffusing components on the diffusion time (diffusion NMR of pulsed-field gradient (PFG) NMR). The analysis has revealed that, at each moment, ~60% of 5-FU molecules form a complex with β-CD and its lifetime is ca. 13.5 ms. It is likely to be an inclusion complex, judging from the independence of the diffusion coefficient of β-CD on complexation. The obtained results could be important for future attempts of finding better methods of targeted anticancer drug delivery.
Collapse
Affiliation(s)
- Daria L. Melnikova
- Institute of Physics, Kazan Federal University, Kremlevskaya 16a, 420111 Kazan, Russia; (D.L.M.); (Z.F.B.)
| | - Zilya F. Badrieva
- Institute of Physics, Kazan Federal University, Kremlevskaya 16a, 420111 Kazan, Russia; (D.L.M.); (Z.F.B.)
| | - Mikhail A. Kostin
- Institute of Chemistry, St. Petersburg State University, Universitetskiy pr. 26, 198504 St. Petersburg, Russia;
| | - Corina Maller
- Institute of Physical and Theoretical Chemistry, Graz University of Technology, NAWI Graz, Stremayrgasse 9, 8010 Graz, Austria; (C.M.); (A.-M.K.)
| | - Monika Stas
- Department of Chemistry, Opole University, Oleska Street 48, 45-052 Opole, Poland; (M.S.); (A.B.); (M.A.B.)
| | - Aneta Buczek
- Department of Chemistry, Opole University, Oleska Street 48, 45-052 Opole, Poland; (M.S.); (A.B.); (M.A.B.)
| | - Malgorzata A. Broda
- Department of Chemistry, Opole University, Oleska Street 48, 45-052 Opole, Poland; (M.S.); (A.B.); (M.A.B.)
| | - Teobald Kupka
- Department of Chemistry, Opole University, Oleska Street 48, 45-052 Opole, Poland; (M.S.); (A.B.); (M.A.B.)
| | - Anne-Marie Kelterer
- Institute of Physical and Theoretical Chemistry, Graz University of Technology, NAWI Graz, Stremayrgasse 9, 8010 Graz, Austria; (C.M.); (A.-M.K.)
| | - Peter M. Tolstoy
- Institute of Chemistry, St. Petersburg State University, Universitetskiy pr. 26, 198504 St. Petersburg, Russia;
| | - Vladimir D. Skirda
- Institute of Physics, Kazan Federal University, Kremlevskaya 16a, 420111 Kazan, Russia; (D.L.M.); (Z.F.B.)
| |
Collapse
|
7
|
Comparative DFT study of inclusion complexes of thymidine-carborane conjugate with β-cyclodextrin and heptakis(2,6-O-dimethyl)-β-cyclodextrin in water. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113767] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
8
|
Adamiak M, Ignaczak A. Quantum chemical study of the complexation process of bis-β-d-glucopyranosyl diazacrown derivative with aspirin and paracetamol molecules. COMPUT THEOR CHEM 2019. [DOI: 10.1016/j.comptc.2019.112591] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
9
|
Encapsulation of alpha-mangostin and hydrophilic beta-cyclodextrins revealed by all-atom molecular dynamics simulations. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.110965] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
10
|
Kerdpol K, Kicuntod J, Wolschann P, Mori S, Rungnim C, Kunaseth M, Okumura H, Kungwan N, Rungrotmongkol T. Cavity Closure of 2-Hydroxypropyl-β-Cyclodextrin: Replica Exchange Molecular Dynamics Simulations. Polymers (Basel) 2019; 11:polym11010145. [PMID: 30960130 PMCID: PMC6401915 DOI: 10.3390/polym11010145] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 01/09/2019] [Accepted: 01/11/2019] [Indexed: 12/15/2022] Open
Abstract
2-Hydroxypropyl-β-cyclodextrin (HPβCD) has unique properties to enhance the stability and the solubility of low water-soluble compounds by inclusion complexation. An understanding of the structural properties of HPβCD and its derivatives, based on the number of 2-hydroxypropyl (HP) substituents at the α-d-glucopyranose subunits is rather important. In this work, replica exchange molecular dynamics simulations were performed to investigate the conformational changes of single- and double-sided HP-substitution, called 6-HPβCDs and 2,6-HPβCDs, respectively. The results show that the glucose subunits in both 6-HPβCDs and 2,6-HPβCDs have a lower chance of flipping than in βCD. Also, HP groups occasionally block the hydrophobic cavity of HPβCDs, thus hindering drug inclusion. We found that HPβCDs with a high number of HP-substitutions are more likely to be blocked, while HPβCDs with double-sided HP-substitutions have an even higher probability of being blocked. Overall, 6-HPβCDs with three and four HP-substitutions are highlighted as the most suitable structures for guest encapsulation, based on our conformational analyses, such as structural distortion, the radius of gyration, circularity, and cavity self-closure of the HPβCDs.
Collapse
Affiliation(s)
- Khanittha Kerdpol
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand.
| | - Jintawee Kicuntod
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
| | - Peter Wolschann
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
- Department of Pharmaceutical Chemistry, University of Vienna, Vienna 1090, Austria.
- Institute of Theoretical Chemistry, University of Vienna, Vienna 1090, Austria.
| | - Seiji Mori
- Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, 2-1-1 Bunkyo, Mito, Ibaraki 310-8512, Japan.
| | - Chompoonut Rungnim
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand.
| | - Manaschai Kunaseth
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand.
| | - Hisashi Okumura
- Research Center for Computational Science, Institute for Molecular Science, Okazaki, Aichi 444-8585, Japan.
| | - Nawee Kungwan
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand.
- Center of Excellence in Materials Science and Technology, Chiang Mai University, Chiang Mai 50200, Thailand.
| | - Thanyada Rungrotmongkol
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
- Ph.D. Program in Bioinformatics and Computational Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
- Molecular Sensory Science Center, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Patumwan, Bangkok 10330, Thailand.
| |
Collapse
|
11
|
Hanpaibool C, Chakcharoensap T, Arifin, Hijikata Y, Irle S, Wolschann P, Kungwan N, Pongsawasdi P, Ounjai P, Rungrotmongkol T. Theoretical analysis of orientations and tautomerization of genistein in β-cyclodextrin. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.05.109] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
|
12
|
The inclusion complexation of daidzein with β-cyclodextrin and 2,6-dimethyl-β-cyclodextrin: a theoretical and experimental study. MONATSHEFTE FUR CHEMIE 2018. [DOI: 10.1007/s00706-018-2209-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
13
|
Khuntawee W, Karttunen M, Wong-Ekkabut J. A molecular dynamics study of conformations of beta-cyclodextrin and its eight derivatives in four different solvents. Phys Chem Chem Phys 2018; 19:24219-24229. [PMID: 28848954 DOI: 10.1039/c7cp04009a] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Understanding the atomic level interactions and the resulting structural characteristics is required for developing beta-cyclodextrin (βCD) derivatives for pharmaceutical and other applications. The effect of four different solvents on the structures of the native βCD and its hydrophilic (methylated βCD; MEβCD and hydroxypropyl βCD; HPβCD) and hydrophobic derivatives (ethylated βCD; ETβCD) was explored using molecular dynamics (MD) simulations and solvation free energy calculations. The native βCD, 2-MEβCD, 6-MEβCD, 2,6-DMβCD, 2,3,6-TMβCD, 6-HPβCD, 2,6-HPβCD and 2,6-ETβCD in non-polar solvents (cyclohexane; CHX and octane; OCT) were stably formed in a symmetric cyclic cavity shape through their intramolecular hydrogen bonds. In contrast, βCDs in polar solvents (methanol; MeOH and water; WAT) exhibited large structural changes and fluctuations leading to significant deformations of their cavities. Hydrogen bonding with polar solvents was found to be one of the major contributors to this behavior: solvent-βCD hydrogen bonding strongly competes with intramolecular bonding leading to significant changes in the structural stability of βCDs. An exception to this is the hydrophobic 2,6-ETβCD which retained its spherical cavity in all solvents. Based on this, it is proposed that the 2,6-ETβCD can act as a sustained release drug carrier.
Collapse
Affiliation(s)
- Wasinee Khuntawee
- Department of Physics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand.
| | | | | |
Collapse
|
14
|
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.
Collapse
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.
| |
Collapse
|
15
|
Wongpituk P, Nutho B, Panman W, Kungwan N, Wolschann P, Rungrotmongkol T, Nunthaboot N. Structural dynamics and binding free energy of neral-cyclodextrins inclusion complexes: molecular dynamics simulation. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1356458] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Peerapong Wongpituk
- Faculty of Science, Department of Chemistry and Center of Excellence for Innovation in Chemistry, Mahasarakham University, Mahasarakham, Thailand
| | - Bodee Nutho
- Faculty of Science, Program in Biotechnology, Chulalongkorn University, Bangkok, Thailand
| | - Wanwisa Panman
- Faculty of Science, Multidisciplinary Program of Petrochemistry and Polymer Science, Chulalongkorn University, Bangkok, Thailand
| | - Nawee Kungwan
- Faculty of Science, Department of Chemistry, Chiang Mai University, Chiang Mai, Thailand
| | - Peter Wolschann
- Faculty of Science, Structural and Computational Biology Research Group, Department of Biochemistry, Chulalongkorn University, Bangkok, Thailand
- Department of Pharmaceutical Technology and Biopharmaceutics, University of Vienna, Vienna, Austria
- Institute of Theoretical Chemistry, University of Vienna, Vienna, Austria
| | - Thanyada Rungrotmongkol
- Faculty of Science, Structural and Computational Biology Research Group, Department of Biochemistry, Chulalongkorn University, Bangkok, Thailand
- Faculty of Science, Ph.D. Program in Bioinformatics and Computational Biology, Chulalongkorn University, Bangkok, Thailand
- Faculty of Science, Molecular Sensory Science Center, Chulalongkorn University, Bangkok, Thailand
| | - Nadtanet Nunthaboot
- Faculty of Science, Department of Chemistry and Center of Excellence for Innovation in Chemistry, Mahasarakham University, Mahasarakham, Thailand
| |
Collapse
|
16
|
Jaiyong P, Bryce RA. Approximate quantum chemical methods for modelling carbohydrate conformation and aromatic interactions: β-cyclodextrin and its adsorption on a single-layer graphene sheet. Phys Chem Chem Phys 2017; 19:15346-15355. [DOI: 10.1039/c7cp02160g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Adsorption of carbohydrates on graphene has the potential to improve graphene dispersibility in water. Here we assess the ability of DFTB-based and NDDO-based quantum chemical methods to model β-cyclodextrin conformations and interactions with graphene.
Collapse
Affiliation(s)
- Panichakorn Jaiyong
- Division of Pharmacy and Optometry
- School of Health Sciences
- Faculty of Biology
- Medicine and Health
- University of Manchester
| | - Richard A. Bryce
- Division of Pharmacy and Optometry
- School of Health Sciences
- Faculty of Biology
- Medicine and Health
- University of Manchester
| |
Collapse
|
17
|
Ignaczak A, Pałecz B, Belica-Pacha S. Quantum chemical study and isothermal titration calorimetry of β-cyclodextrin complexes with mianserin in aqueous solution. Org Biomol Chem 2017; 15:1209-1216. [DOI: 10.1039/c6ob02109c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The structures, interaction energies and thermodynamics of the complex formation between mianserin (MIA) and β-cyclodextrin (β-CD) are investigated using computational methods and calorimetric measurements.
Collapse
Affiliation(s)
- Anna Ignaczak
- Department of Theoretical and Structural Chemistry
- Faculty of Chemistry
- University of Lodz
- 90-236 Lodz
- Poland
| | - Bartłomiej Pałecz
- Unit of Biophysical Chemistry
- Department of Physical Chemistry
- Faculty of Chemistry
- University of Lodz
- 90-236 Lodz
| | - Sylwia Belica-Pacha
- Unit of Biophysical Chemistry
- Department of Physical Chemistry
- Faculty of Chemistry
- University of Lodz
- 90-236 Lodz
| |
Collapse
|
18
|
Nutho B, Nunthaboot N, Wolschann P, Kungwan N, Rungrotmongkol T. Metadynamics supports molecular dynamics simulation-based binding affinities of eucalyptol and beta-cyclodextrin inclusion complexes. RSC Adv 2017. [DOI: 10.1039/c7ra09387j] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The development of various molecular dynamics methods enables the detailed investigation of association processes, like host–guest complexes, including their dynamics and, additionally, the release of the guest compound.
Collapse
Affiliation(s)
- Bodee Nutho
- Program in Biotechnology
- Faculty of Science
- Chulalongkorn University
- Bangkok 10330
- Thailand
| | - Nadtanet Nunthaboot
- Department of Chemistry
- Center of Excellence for Innovation in Chemistry
- Faculty of Science
- Mahasarakham University
- Mahasarakham 44150
| | - Peter Wolschann
- Structural and Computational Biology Research Group
- Department of Biochemistry
- Faculty of Science
- Chulalongkorn University
- Bangkok 10330
| | - Nawee Kungwan
- Department of Chemistry
- Faculty of Science
- Chiang Mai University
- Chiang Mai 50200
- Thailand
| | - Thanyada Rungrotmongkol
- Structural and Computational Biology Research Group
- Department of Biochemistry
- Faculty of Science
- Chulalongkorn University
- Bangkok 10330
| |
Collapse
|
19
|
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.
Collapse
|
20
|
Kicuntod J, Khuntawee W, Wolschann P, Pongsawasdi P, Chavasiri W, Kungwan N, Rungrotmongkol T. Inclusion complexation of pinostrobin with various cyclodextrin derivatives. J Mol Graph Model 2015; 63:91-8. [PMID: 26709752 DOI: 10.1016/j.jmgm.2015.11.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 11/03/2015] [Accepted: 11/06/2015] [Indexed: 01/07/2023]
Abstract
Pinostrobin (PNS) is one of the important flavonoids and can be abundantly found in the rhizomes of fingerroot (Boesenbergia rotrunda) and galangal (Alpinia galangal and Alpinia officinarum), the herbal basis of Southeast Asian cooking. Similar to other flavonoids, PNS exhibits anti-oxidative, anti-inflammatory and anti-cancer properties. However, this compound has an extremely low water solubility that limits its use in pharmaceutical applications. Beta-cyclodextrin (βCD) and its derivatives, 2,6-dimethyl-βCD (2,6-DMβCD) and the three hydroxypropyl-βCDs (2-HPβCD, 6-HPβCD and 2,6-DHPβCD), have unique properties that enhance the stability and solubility of such low-soluble guest molecules. In the present study, molecular dynamics simulations were applied to investigate the dynamics and stability of PNS inclusion complexes with βCD and its derivatives (2,6-DMβCD, 2,6-DHPβCD, 2-HPβCD and 6-HPβCD). PNS was able to form complexes with βCD and all four of its derivatives by either the chromone (C-PNS) or phenyl (P-PNS) ring dipping toward the cavity. According to the molecular mechanics-generalized Born surface area binding free energy values, the stability of the different PNS/βCD complexes was ranked as 2,6-DHPβCD>2,6-DMβCD>2-HPβCD>6-HPβCD>βCD. These theoretical results were in good agreement with the stability constants that had been determined by the solubility method.
Collapse
Affiliation(s)
- Jintawee Kicuntod
- Structural and Computational Biology Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; Starch and Cyclodextrin Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Wasinee Khuntawee
- Nanoscience and Technology Program, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand
| | - Peter Wolschann
- Structural and Computational Biology Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; Department of Pharmaceutical Technology and Biopharmaceutics, University of Vienna, Vienna 1090, Austria; Institute of Theoretical Chemistry, University of Vienna, Vienna 1090, Austria
| | - Piamsook Pongsawasdi
- Starch and Cyclodextrin Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Warinthorn Chavasiri
- Natural Products Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Nawee Kungwan
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Thanyada Rungrotmongkol
- Structural and Computational Biology Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; Program in Bioinformatics and Computational Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
| |
Collapse
|
21
|
Przybylski C, Bonnet V, Cézard C. Probing the common alkali metal affinity of native and variously methylated β-cyclodextrins by combining electrospray-tandem mass spectrometry and molecular modeling. Phys Chem Chem Phys 2015; 17:19288-305. [PMID: 26138713 DOI: 10.1039/c5cp02895g] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
In the study herein, we investigated the solution and gas phase affinity of native and variously methylated β-cyclodextrins (CDs) as hosts towards three common alkali metals as guests namely lithium, sodium and potassium. For this purpose, two complementary approaches have been employed: electrospray-tandem mass spectrometry (ESI-MS/MS) with two energetic regimes: Collision Induced Dissociation (CID) and Higher Collision Dissociation (HCD), respectively, and DFT molecular modeling. These approaches have been achieved by taking into account the interaction of either one or two alkali metals with the host molecules. The results showed a good agreement between experimental and theoretical data. It was demonstrated that increasing the methylation degree strengthened the gas phase affinity towards all studied alkali metals. Furthermore, it was established that the cation selectivity was Na(+) > Li(+) > K(+) and Li(+) > Na(+) > K(+) for the solution and gas phase, respectively.
Collapse
Affiliation(s)
- Cédric Przybylski
- Université d'Evry-Val-d'Essonne, Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, CNRS UMR 8587, Bâtiment Maupertuis, Bld F. Mitterrand, F-91025 Evry, France.
| | | | | |
Collapse
|
22
|
Khuntawee W, Wolschann P, Rungrotmongkol T, Wong-ekkabut J, Hannongbua S. Molecular Dynamics Simulations of the Interaction of Beta Cyclodextrin with a Lipid Bilayer. J Chem Inf Model 2015; 55:1894-902. [DOI: 10.1021/acs.jcim.5b00152] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Peter Wolschann
- Department
of Pharmaceutical Technology and Biopharmaceutics, University of Vienna, 14 Althan Straße 14, Vienna 1090, Austria
- Institute
of Theoretical Chemistry, University of Vienna, Währinger
Straße 17, Vienna 1090, Austria
| | | | - Jirasak Wong-ekkabut
- Department
of Physics, Faculty of Science, Kasetsart University, 50 Phahon
Yothin Road, Chatuchak, Bangkok 10900, Thailand
| | | |
Collapse
|
23
|
Lee SS, Park S, Kim JY, Kim HR, Lee S, Oh HB. Infrared multiple photon dissociation spectroscopy and density functional theory (DFT) studies of protonated permethylated β-cyclodextrin-water non-covalent complexes. Phys Chem Chem Phys 2015; 16:8376-83. [PMID: 24658048 DOI: 10.1039/c3cp54841d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present infrared multiple photon dissociation (IRMPD) spectroscopy and quantum chemical calculation results for the protonated permethylated β-cyclodextrin (CD)-water non-covalent complex, the simplest β-CD non-covalent complex, in the gas-phase. The IRMPD spectrum in the region 2700-3750 cm(-1) consisted of three strong peaks at 3096, 3315, and 3490 cm(-1). These spectral features in the experimental IRMPD spectrum were compared with a large set of infrared absorption spectra predicted using density functional theory (DFT) calculations for the protonated β-CD-water complex. Complex III (see ), in which the water molecule (at the primary rim) and the proton (at the secondary rim) were separated, was found to suitably reflect the main spectral characteristics found in the experimental IRMPD spectrum. The absence of the homodromic hydrogen bond ring, due to replacement of hydroxyl groups with methoxy groups in permethylated β-CD, rendered the primary rim open compared with the unmodified β-CD 'one-gate-closed' lowest energy conformer. This study demonstrates that IRMPD studies combined with DFT theoretical calculations can be a good method for studying molecular interactions of large host-guest pairs.
Collapse
Affiliation(s)
- Sung-Sik Lee
- Department of Applied Chemistry, Kyung Hee University, Gyeonggi 446-701, Korea.
| | | | | | | | | | | |
Collapse
|
24
|
Nutho B, Khuntawee W, Rungnim C, Pongsawasdi P, Wolschann P, Karpfen A, Kungwan N, Rungrotmongkol T. Binding mode and free energy prediction of fisetin/β-cyclodextrin inclusion complexes. Beilstein J Org Chem 2014; 10:2789-99. [PMID: 25550745 PMCID: PMC4273227 DOI: 10.3762/bjoc.10.296] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Accepted: 11/06/2014] [Indexed: 12/26/2022] Open
Abstract
In the present study, our aim is to investigate the preferential binding mode and encapsulation of the flavonoid fisetin in the nano-pore of β-cyclodextrin (β-CD) at the molecular level using various theoretical approaches: molecular docking, molecular dynamics (MD) simulations and binding free energy calculations. The molecular docking suggested four possible fisetin orientations in the cavity through its chromone or phenyl ring with two different geometries of fisetin due to the rotatable bond between the two rings. From the multiple MD results, the phenyl ring of fisetin favours its inclusion into the β-CD cavity, whilst less binding or even unbinding preference was observed in the complexes where the larger chromone ring is located in the cavity. All MM- and QM-PBSA/GBSA free energy predictions supported the more stable fisetin/β-CD complex of the bound phenyl ring. Van der Waals interaction is the key force in forming the complexes. In addition, the quantum mechanics calculations with M06-2X/6-31G(d,p) clearly showed that both solvation effect and BSSE correction cannot be neglected for the energy determination of the chosen system.
Collapse
Affiliation(s)
- Bodee Nutho
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Wasinee Khuntawee
- Nanoscience and Technology Program, Graduate School, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Chompoonut Rungnim
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Thanon Phahonyothin Tambon Khlong Nueng, Amphoe Khlong Luang, Pathum Thani 12120, Thailand
| | - Piamsook Pongsawasdi
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Peter Wolschann
- Department of Pharmaceutical Technology and Biopharmaceutics, University of Vienna, Vienna 1090, Austria ; Institute of Theoretical Chemistry, University of Vienna, Vienna 1090, Austria
| | - Alfred Karpfen
- Institute of Theoretical Chemistry, University of Vienna, Vienna 1090, Austria
| | - Nawee Kungwan
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Thanyada Rungrotmongkol
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| |
Collapse
|
25
|
Sangpheak W, Khuntawee W, Wolschann P, Pongsawasdi P, Rungrotmongkol T. Enhanced stability of a naringenin/2,6-dimethyl β-cyclodextrin inclusion complex: molecular dynamics and free energy calculations based on MM- and QM-PBSA/GBSA. J Mol Graph Model 2014; 50:10-5. [PMID: 24681901 DOI: 10.1016/j.jmgm.2014.03.001] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 02/27/2014] [Accepted: 03/01/2014] [Indexed: 10/25/2022]
Abstract
The structure, dynamic behavior and binding affinity of the inclusion complexes between naringenin and the two cyclodextrins (CDs), β-CD and its 2,6-dimethyl derivative (DM-β-CD), were theoretically studied by multiple molecular dynamics simulations and free energy calculations. Naringenin most likely prefers to bind with CDs through the phenyl ring. Although a lower hydrogen bond formation of naringenin with the 3-hydroxyl group of DM-β-CD (relative to β-CD) was observed, the higher cavity could encapsulate almost the whole naringenin molecule. In contrast for the naringenin/β-CD complex, the phenyl ring feasibly passed through the primary rim resulting in the chromone ring binding inside instead. MM-PBSA/GBSA and QM-PBSA/GBSA binding free energies strongly suggested a greater stability of the naringenin/DM-β-CD inclusion complex. Van der Waals force played an important role as the key guest-host interaction for the complexation between naringenin and each cyclodextrin.
Collapse
Affiliation(s)
- Waratchada Sangpheak
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Wasinee Khuntawee
- Nanoscience and Technology Program, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand
| | - Peter Wolschann
- Department of Pharmaceutical Technology and Biopharmaceutics, University of Vienna, Vienna 1090, Austria; Institute of Theoretical Chemistry, University of Vienna, Vienna 1090, Austria
| | - Piamsook Pongsawasdi
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Thanyada Rungrotmongkol
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
| |
Collapse
|
26
|
Yao L, Mori Y, Takano K. Theoretical Study on Intermolecular Interactions in Complexes of Cyclodextrins with Bile Acids: DFT and Ab Initio Fragment Molecular Orbital Calculations. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2014. [DOI: 10.1246/bcsj.20130205] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Lan Yao
- Department of Chemistry and Biochemistry, Graduate School of Humanities and Sciences, Ochanomizu University
| | - Yukie Mori
- Department of Chemistry, Faculty of Science, Ochanomizu University
| | - Keiko Takano
- Department of Chemistry and Biochemistry, Graduate School of Humanities and Sciences, Ochanomizu University
| |
Collapse
|
27
|
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.
Collapse
Affiliation(s)
- Qi Yao
- School of Chemistry and Chemical engineering, Wuhan Textile University, 430073 Wuhan, China
| | | | | | | | | | | |
Collapse
|
28
|
Stachowicz A, Rogalski M, Korchowiec J. Charge sensitivity approach to mutual polarization of reactants: molecular mechanics perspective. J Mol Model 2013; 19:4163-72. [PMID: 23392762 PMCID: PMC4271185 DOI: 10.1007/s00894-013-1757-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2012] [Accepted: 01/03/2013] [Indexed: 11/26/2022]
Abstract
Charge sensitivity analysis (CSA) in force-field atoms resolution was applied to describe the mutual polarization of reactants as well as charge-transfer (CT) effects. An inclusion complex of β-cyclodextrin with salicylic acid was used as a model system. Three CSA models were taken into account and verified on a Born–Oppenheimer molecular dynamics (BOMD) trajectory. The models differed in terms of the equilibrium conditions imposed on the system. It was demonstrated that mutual polarization is an important source of stabilization, in contrast to the results obtained from static charge calculations. The energy lowering induced by CT was small and comparable to the CT stabilization that occurs in hydrogen-bonded systems. All models correctly described the main topological features of the BOMD energy surface. CSA in force-field atoms resolution qualitatively reproduced the charge reorganization accompanying hydrogen-bond formation. It was shown that CSA parameters are very sensitive to the bond formation process, which suggests that they could be applied in reactive force fields as detectors of newly formed chemical bonds. Fukui function detector of bond formation during molecular dynamics simulations of inclusion complex of b-cyclodextrin with salicylic acid. ![]()
Collapse
Affiliation(s)
- Anna Stachowicz
- K. Gumiński Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, R. Ingardena 3, Kraków, Poland
| | - Marek Rogalski
- Laboratoire de Chimie et Physique - Approche Multi-Echelle des Milieux Complexes, EA 4164, Université de Lorraine, 1 Boulevard Arago, 57070 Metz, France
| | - Jacek Korchowiec
- K. Gumiński Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, R. Ingardena 3, Kraków, Poland
| |
Collapse
|
29
|
Voskuhl J, Waller M, Bandaru S, Tkachenko BA, Fregonese C, Wibbeling B, Schreiner PR, Ravoo BJ. Nanodiamonds in sugar rings: an experimental and theoretical investigation of cyclodextrin–nanodiamond inclusion complexes. Org Biomol Chem 2012; 10:4524-30. [DOI: 10.1039/c2ob06915f] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
30
|
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]
|
31
|
Deshmukh MM, Bartolotti LJ, Gadre SR. Intramolecular hydrogen bond energy and cooperative interactions in α-, β-, and γ-cyclodextrin conformers. J Comput Chem 2011; 32:2996-3004. [PMID: 21793006 DOI: 10.1002/jcc.21881] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Revised: 06/15/2011] [Accepted: 06/17/2011] [Indexed: 11/10/2022]
Abstract
Accurate estimation of individual intramolecular hydrogen bond (H-bond) energies is an intricate task for multiply H-bonded systems. In such cases, the hydrogen bond strengths could be highly influenced by the cooperative interactions, for example, those between hydroxyl groups in sugars. In this work, we use the recently proposed molecular tailoring approach-based quantification (Deshmukh, Gadre, and Bartolotti, J Phys Chem A 2006, 110, 12519) to the extended systems of cyclodextrins (CDs). Further, the structure and stability of different conformers of α-, β-, and γ-CDs are explained based on the energetics and cooperative contribution to the strength of these H-bonds. The estimated O-H···O H-bond energies in the various CD conformers are found to vary widely from 1.1 to 8.3 kcal mol(-1). The calculated energy contributions to cooperativity toward the H-bond strengths fall in the range of 0.25-2.75 kcal mol(-1).
Collapse
|
32
|
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]
|
33
|
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]
|
34
|
Boonyarattanakalin KS, Wolschann P, Lawtrakul L. Molecular dynamics of β-CD in water/co-solvent mixtures. J INCL PHENOM MACRO 2011. [DOI: 10.1007/s10847-010-9913-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
35
|
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]
|
36
|
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]
|
37
|
Naidoo KJ, Gamieldien MR, Chen JYJ, Widmalm G, Maliniak A. Glucose Orientation and Dynamics in α-, β-, and γ-Cyclodextrins. J Phys Chem B 2008; 112:15151-7. [DOI: 10.1021/jp805174y] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kevin J. Naidoo
- Department of Chemistry, University of Cape Town, Rondebosch, 7701, South Africa., Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden., Division of Physical Chemistry Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| | - M. Riedaa Gamieldien
- Department of Chemistry, University of Cape Town, Rondebosch, 7701, South Africa., Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden., Division of Physical Chemistry Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| | - Jeff Yu-Jen Chen
- Department of Chemistry, University of Cape Town, Rondebosch, 7701, South Africa., Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden., Division of Physical Chemistry Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| | - Göran Widmalm
- Department of Chemistry, University of Cape Town, Rondebosch, 7701, South Africa., Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden., Division of Physical Chemistry Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| | - Arnold Maliniak
- Department of Chemistry, University of Cape Town, Rondebosch, 7701, South Africa., Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden., Division of Physical Chemistry Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| |
Collapse
|
38
|
Rodriguez J, Hernán Rico D, Domenianni L, Laria D. Confinement of Polar Solvents within β-Cyclodextrins. J Phys Chem B 2008; 112:7522-9. [DOI: 10.1021/jp711609q] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Javier Rodriguez
- Departamento de Química Inorgánica, Analítica y Química-Física e INQUIMAE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón II, 1428, Buenos Aires, Argentina, and Departamento de Física, Comisión Nacional de Energía Atómica, Avenida Libertador 8250, 1429, Buenos Aires, Argentina
| | - Daniel Hernán Rico
- Departamento de Química Inorgánica, Analítica y Química-Física e INQUIMAE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón II, 1428, Buenos Aires, Argentina, and Departamento de Física, Comisión Nacional de Energía Atómica, Avenida Libertador 8250, 1429, Buenos Aires, Argentina
| | - Luis Domenianni
- Departamento de Química Inorgánica, Analítica y Química-Física e INQUIMAE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón II, 1428, Buenos Aires, Argentina, and Departamento de Física, Comisión Nacional de Energía Atómica, Avenida Libertador 8250, 1429, Buenos Aires, Argentina
| | - Daniel Laria
- Departamento de Química Inorgánica, Analítica y Química-Física e INQUIMAE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón II, 1428, Buenos Aires, Argentina, and Departamento de Física, Comisión Nacional de Energía Atómica, Avenida Libertador 8250, 1429, Buenos Aires, Argentina
| |
Collapse
|
39
|
|
40
|
Pinjari RV, Joshi KA, Gejji SP. Theoretical studies on hydrogen bonding, NMR chemical shifts and electron density topography in alpha, beta and gamma-cyclodextrin conformers. J Phys Chem A 2007; 111:13583-9. [PMID: 18052135 DOI: 10.1021/jp074539w] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrogen-bonded interactions in alpha-, beta-, and gamma-CD conformers are investigated from the molecular electron density topography and chemical shift in the nuclear magnetic resonance (NMR) spectra calculated by using the Gauge Invariant Atomic Orbital (GIAO) method within the framework of density functional theory. For the lowest-energy CD conformers in the gas phase, the O3-H...O2' hydrogen-bonding interactions are present. Calculated 1H NMR chemical shifts (delta H) correlate well with the hydrogen-bond distance as well as electron density at the bond critical point in the molecular electron density (MED) topography. The conformers of beta- and gamma-CD comprised of relatively strong secondary hydroxyl interactions are stabilized by solvation from polar solvents.
Collapse
Affiliation(s)
- Rahul V Pinjari
- Department of Chemistry, University of Pune, Ganeshkhind 411007, Pune, India
| | | | | |
Collapse
|