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Raffaini G, Elli S, Catauro M, D’Angelo A. Different Drug Mobilities in Hydrophobic Cavities of Host-Guest Complexes between β-Cyclodextrin and 5-Fluorouracil at Different Stoichiometries: A Molecular Dynamics Study in Water. Int J Mol Sci 2024; 25:5888. [PMID: 38892075 PMCID: PMC11172661 DOI: 10.3390/ijms25115888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 05/11/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024] Open
Abstract
Cyclodextrins (CDs) are cyclic oligosaccharides able to form noncovalent water-soluble complexes useful in many different applications for the solubilization, delivery, and greater bioavailability of hydrophobic drugs. The complexation of 5-fluorouracil (5-FU) with natural or synthetic cyclodextrins permits the solubilization of this poorly soluble anticancer drug. In this theoretical work, the complexes between β-CD and 5-FU are investigated using molecular mechanics (MM) and molecular dynamics (MD) simulations in water. The inclusion complexes are formed thanks to the favorable intermolecular interactions between β-CD and 5-FU. Both 1:1 and 1:2 β-CD/5-FU stoichiometries are investigated, providing insight into their interaction geometries and stability over time in water. In the 1:2 β-CD/5-FU complexes, the intermolecular interactions affect the drug's mobility, suggesting a two-step release mechanism: a fast release for the more exposed and hydrated drug molecule, with greater freedom of movement near the β-CD rims, and a slow one for the less-hydrated and well-encapsulated and confined drug. MD simulations study the intermolecular interactions between drugs and specific carriers at the atomistic level, suggesting a possible release mechanism and highlighting the role of the impact of the drug concentration on the kinetics process in water. A comparison with experimental data in the literature provides further insights.
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Affiliation(s)
- Giuseppina Raffaini
- Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta”, Politecnico di Milano, Piazza L. Da Vinci 32, 20131 Milano, Italy
- INSTM, National Consortium of Materials Science and Technology, Local Unit Politecnico di Milano, 50121 Milano, Italy
| | - Stefano Elli
- Istituto di Ricerche Chimiche e Biochimiche ‘G. Ronzoni’, Via Giuseppe Colombo 81, 20133 Milano, Italy;
| | - Michelina Catauro
- Department of Engineering, University of Campania “Luigi Vanvitelli”, Via Roma 29, 81031 Aversa, Italy; (M.C.); (A.D.)
| | - Antonio D’Angelo
- Department of Engineering, University of Campania “Luigi Vanvitelli”, Via Roma 29, 81031 Aversa, Italy; (M.C.); (A.D.)
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Buczek A, Rzepiela K, Kupka T, Broda MA, Kar T. Uracil-water interaction revisited - in search of single H-bonded secondary minima. Phys Chem Chem Phys 2024; 26:5169-5182. [PMID: 38261334 DOI: 10.1039/d3cp04057g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Monohydrated uracil (UW) complexes are stabilized by both O⋯HO and NH⋯O hydrogen bonds (H-bonds), simultaneously participating in forming three stable cyclic structures. The role and contribution of these individual H-bonds (O⋯HO and NH⋯O) to the stability of the three UW complexes are still not understood, because of the technical problems in obtaining their optimized structures by standard geometry optimization. The present study explores a non-standard approach to identify three single H-bonded local minima structures without imaginary frequency using DFT (M06-2X, B3LYP and B3LYP-D3), MP2 and CCSD(T) theories and Dunning's correlation-consistent aug-cc-pVTZ basis set, in both vacuum and aqueous media (CPCM method). The results reveal that these new structures are very shallow secondary minima between two deep wells or next to a deep well of primary minima (double H-bonded structures) in the potential energy surface. The H-bond energy of these single H-bonded complexes is found to be less sensitive to a wide range (about 15-20 degrees) of O⋯HO and NH⋯O angles, and the linearity is preferred in the stable three single H-bonded structures. The technical method used to locate such a shallow minimum is described in detail and may be useful for identifying local minima in other cases where consecutive multiple H-bonded structures are global minima. Energy decomposition (using symmetry adapted perturbation theory (SAPT)) of interaction energy, electron redistribution, and relevant vibrational modes are discussed.
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Affiliation(s)
- Aneta Buczek
- Faculty of Chemistry, University of Opole, Oleska 48, 45-052 Opole, Poland.
| | - Kacper Rzepiela
- Faculty of Chemistry, University of Opole, Oleska 48, 45-052 Opole, Poland.
| | - Teobald Kupka
- Faculty of Chemistry, University of Opole, Oleska 48, 45-052 Opole, Poland.
| | - Małgorzata A Broda
- Faculty of Chemistry, University of Opole, Oleska 48, 45-052 Opole, Poland.
| | - Tapas Kar
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322, USA.
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Hansen PE. The Synergy between Nuclear Magnetic Resonance and Density Functional Theory Calculations. Molecules 2024; 29:336. [PMID: 38257249 PMCID: PMC10821511 DOI: 10.3390/molecules29020336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
This paper deals with the synergy between Nuclear Magnetic Resonance (NMR) spectroscopic investigations and DFT calculations, mainly of NMR parameters. Both the liquid and the solid states are discussed here. This text is a mix of published results supplemented with new findings. This paper deals with examples in which useful results could not have been obtained without combining NMR measurements and DFT calculations. Examples of such cases are tautomeric systems in which NMR data are calculated for the tautomers; hydrogen-bonded systems in which better XH bond lengths can be determined; cage compounds for which assignment cannot be made based on NMR data alone; revison of already published structures; ionic compounds for which reference data are not available; assignment of solid-state spectra and crystal forms; and the creation of libraries for biological molecules. In addition to these literature cases, a revision of a cage structure and substituent effects on pyrroles is also discussed.
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Affiliation(s)
- Poul Erik Hansen
- Department of Science and Environment, Roskilde University, DK-4000 Roskilde, Denmark
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Rzepiela K, Kaminský J, Buczek A, Broda MA, Kupka T. Electron Correlation or Basis Set Quality: How to Obtain Converged and Accurate NMR Shieldings for the Third-Row Elements? MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238230. [PMID: 36500321 PMCID: PMC9737175 DOI: 10.3390/molecules27238230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/17/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022]
Abstract
The quality of theoretical NMR shieldings calculated at the quantum-chemical level depends on various theoretical aspects, of which the basis set type and size are among the most important factors. Nevertheless, not much information is available on the basis set effect on theoretical shieldings of the NMR-active nuclei of the third row. Here, we report on the importance of proper basis set selection to obtain accurate and reliable NMR shielding parameters for nuclei from the third row of the periodic table. All calculations were performed on a set of eleven compounds containing the elements Na, Mg, Al, Si, P, S, or Cl. NMR shielding tensors were calculated using the SCF-HF, DFT-B3LYP, and CCSD(T) methods, combined with the Dunning valence aug-cc-pVXZ, core-valence aug-cc-pCVXZ, Jensen polarized-convergent aug-pcSseg-n and Karlsruhe x2c-Def2 basis set families. We also estimated the complete basis set limit (CBS) values of the NMR parameters. Widely scattered nuclear shieldings were observed for the Dunning polarized-valence basis set, which provides irregular convergence. We show that the use of Dunning core-valence or Jensen basis sets effectively reduces the scatter of theoretical NMR results and leads to their exponential-like convergence to CBS. We also assessed the effect of vibrational, temperature, and relativistic corrections on the predicted shieldings. For systems with single bonds, all corrections are relatively small, amounting to less than 4% of the CCSD(T)/CBS value. Vibrational and temperature corrections were less reliable for H3PO and HSiCH due to the high anharmonicity of the molecules. An abnormally high relativistic correction was observed for phosphorus in PN, reaching ~20% of the CCSD(T)/CBS value, while the correction was less than 7% for other tested molecules.
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Affiliation(s)
- Kacper Rzepiela
- Faculty of Chemistry, University of Opole, 48 Oleska Street, 46-052 Opole, Poland
| | - Jakub Kaminský
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám. 2, 166 10 Prague, Czech Republic
- Correspondence: (J.K.); (T.K.)
| | - Aneta Buczek
- Faculty of Chemistry, University of Opole, 48 Oleska Street, 46-052 Opole, Poland
| | - Małgorzata A. Broda
- Faculty of Chemistry, University of Opole, 48 Oleska Street, 46-052 Opole, Poland
| | - Teobald Kupka
- Faculty of Chemistry, University of Opole, 48 Oleska Street, 46-052 Opole, Poland
- Correspondence: (J.K.); (T.K.)
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Buczek A, Kupka T, Broda MA, Maślanka S, Pentak D. Liposomes as nonspecific nanocarriers for 5-Fluorouracil in the presence of cyclodextrins. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117623] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Carbazole derivatives: Synthesis, spectroscopic characterization, antioxidant activity, molecular docking study, and the quantum chemical calculations. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115651] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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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.
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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.)
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On the aromaticity of uracil and its 5-halogeno derivatives as revealed by theoretically derived geometric and magnetic indexes. Struct Chem 2020. [DOI: 10.1007/s11224-020-01682-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
AbstractThe problem of aromaticity in heterocyclic rings of uracil and its 5-halogenoderivatives (5XU) was analyzed theoretically by calculating modified harmonic oscillator model of aromaticity (HOMA) for Heterocycle Electron Delocalization (HOMHED), nucleus-independent chemical shift parameters (NICS) and the so-called scan experiments, using helium-3 atom as a magnetic probe. The impact of halogen electronegativity on C5 atom’s NBO charges was also investigated. Water, as a polar environment, has a negligible impact on 5XU aromaticity. The most stable diketo tautomer shows a very low aromaticity while the “rare” dihydroxy form (tautomer No 6) is aromatic and resembles benzene. This is in agreement with traditional drawing of chemical formula of uracil’s six-membered ring, directly showing three alternating single and double bonds in its tautomer No 6. No good correlation between magnetic and geometric indexes of aromaticity for the studied 5XU tautomers was found. Linear correlation between the magnitude of NICS minimum, as well as the distance of the minimum above uracil ring plane center from 3He NMR chemical shift scan plot with respect to halogen electronegativity were observed. A strong linear dependence of magnetic index of aromaticity and the electronegativity of 5X substituent was observed.
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