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Kumar P, Purohit R. Driving forces and large scale affinity calculations for piperine/γ-cyclodxetrin complexes: Mechanistic insights from umbrella sampling simulation and DFT calculations. Carbohydr Polym 2024; 342:122350. [PMID: 39048216 DOI: 10.1016/j.carbpol.2024.122350] [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: 01/27/2024] [Revised: 05/13/2024] [Accepted: 05/29/2024] [Indexed: 07/27/2024]
Abstract
Piperine (PiP), a bioactive molecule, exhibits numerous health benefits and is frequently employed as a co-delivery agent with various phytomedicines (e.g., curcumin) to enhance their bioavailability. This is attributed to PiP's inhibitory activity against drug-metabolizing proteins, notably CYP3A4. Nevertheless, PiP encounters solubility challenges addressed in this study using cyclodextrins (CDs). Specifically, γ-CD and its derivatives, Hydroxypropyl-γ-CD (HP-γ-CD), and Octakis (6-O-sulfo)-γ-CD (Octakis-S-γ-CD), were employed to form supramolecular complexes with PiP. The conformational space of the complexes was assessed through 1 μs molecular dynamics simulations and umbrella sampling. Additionally, quantum mechanical calculations using wB97X-D dispersion-corrected DFT functional and 6-311 + G(d,p) basis set were conducted on the complexes to examine the thermodynamics and kinetic stability. Results indicated that Octakis-S-γ-CD exhibits superior host capabilities for PiP, with the most favorable complexation energy (-457.05 kJ/mol), followed by HP-γ-CD (-249.16 kJ/mol). Furthermore, two conformations of the Octakis-S-γ-CD/PiP complex were explored to elucidate the optimal binding orientation of PiP within the binding pocket of Octakis-S-γ-CD. Supramolecular chemistry relies significantly on non-covalent interactions. Therefore, our investigation extensively explores the critical atoms involved in these interactions, elucidating the influence of substituted groups on the stability of inclusion complexes. This comprehensive analysis contributes to emphasizing the γ-CD derivatives with improved host capacity.
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Affiliation(s)
- Pramod Kumar
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP 176061, India; Biotechnology division, CSIR-IHBT, Palampur, HP 176061, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Rituraj Purohit
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP 176061, India; Biotechnology division, CSIR-IHBT, Palampur, HP 176061, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India.
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2
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Roth E, Listyarini RV, Hofer TS, Cziferszky M. Host-Guest Interactions of Ruthenium(II) Arene Complexes with Cucurbit[7/8]uril. Inorg Chem 2024; 63:14021-14031. [PMID: 39016439 PMCID: PMC11289748 DOI: 10.1021/acs.inorgchem.4c01755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 07/10/2024] [Accepted: 07/11/2024] [Indexed: 07/18/2024]
Abstract
Cucurbit[n]urils (CB[n]s) have been recognized for their chemical and thermal stability, and their ability to bind many neutral and cationic guest molecules makes them excellent hosts in a range of supramolecular applications. In drug delivery, CB[n]s can enhance drug solubility, improve chemical and physical drug stability, and allow for triggered and controlled release. This study aimed to investigate the ability of CB[7] and CB[8] as molecular hosts to bind ruthenium(II) arene complexes that are current anticancer lead structures in the area of metallodrugs. Both, experimental and computational methods, led to insights into the binding preferences and geometries of [RuII(cym)Cl2]2 (1; cym = η6-p-cymene), [RuII(cym)(dmb)Cl2]) (2; cym = η6-p-cymene; dmb = 1,3-dimethylbenzimidazol-2-ylidene), and [RuII(cym)(pta)Cl2] (3, RAPTA-C; cym = η6-p-cymene; pta = 1,3,5-triaza-7-phospha-adamantane) with CB[7] and CB[8]. Competition experiments by mass spectrometry revealed clear preferences of 2 for CB[8] and 3 for CB[7]. Based on a comparison of the associated interaction energies from quantum chemical calculations as well as experimental data, 3@CB[7] clearly prefers a binding mode, where the pta ligand is located inside the cavity of the host, and the metal ion interacts with two of the carbonyl groups on the rim of CB[7]. In contrast, complex 2 binds in two different orientations with interaction energies similar to those of both CB[n]s, with the cym ligand being either inside or outside of the cavity. These findings suggest that ruthenium(II) arene complexes are able to form stable host-guest interactions with CB[n]s, which can be exploited as drug delivery vehicles in further metallodrug development to improve their chemical stability.
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Affiliation(s)
- Elisa Roth
- Institute
for Pharmacy, Pharmaceutical Chemistry, Department of Chemistry and
Pharmacy, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Risnita Vicky Listyarini
- Institute
of General, Inorganic and Theoretical Chemistry, Center for Chemistry
and Biomedicine, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
- Chemistry
Education Study Program, Sanata Dharma University, Yogyakarta 55282, Indonesia
| | - Thomas S. Hofer
- Institute
of General, Inorganic and Theoretical Chemistry, Center for Chemistry
and Biomedicine, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Monika Cziferszky
- Institute
for Pharmacy, Pharmaceutical Chemistry, Department of Chemistry and
Pharmacy, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
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3
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Kumar P, Bhardwaj VK, Purohit R. Dispersion-corrected DFT calculations and umbrella sampling simulations to investigate stability of Chrysin-cyclodextrin inclusion complexes. Carbohydr Polym 2023; 319:121162. [PMID: 37567706 DOI: 10.1016/j.carbpol.2023.121162] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/08/2023] [Accepted: 06/27/2023] [Indexed: 08/13/2023]
Abstract
The study of inclusion complexes of Chrysin (ChR) with three forms of cyclodextrins (CDs) α-, β-, and γ-CD was accomplished to examine the stability of ChR inside the central cavities of CDs. The aim of study was to identify the most suitable form of CD to improve the hydro-solubility of poorly soluble ChR bioactive molecule. Microsecond timescale molecular dynamics (MD) simulations were performed on four inclusion complexes (α-CD/ChR, β-CD/ChR, and two conformations of γ-CD/ChR) to examine the dynamics of ChR inside the cavity of CDs. The first conformation of γ-CD/ChR inclusion complex (γ-CD1/ChR) was identified to possess the highest affinity between host and guest molecule on the basis of binding energy calculated by employing Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) and umbrella sampling simulations. To further strengthen the claims of classical and biased MD studies, Our own N-layered Integrated molecular Orbital and Molecular mechanics (ONIOM) (wB97XD/6-311+g(d,p):pm7) calculations were performed on the selected inclusion complexes. The ONIOM based complexation energy reaffirmed that ChR had highest affinity for the γ-CD1 host molecule. Further, the non-covalent interaction analysis was conducted using Multiwfn software on QM-optimized inclusion complexes with wB97XD/6-311+G(d,p) model chemistry, revealing non-covalent interactions between ChR and CDs. This atomic level information helped us to gain better insights into critical atoms of ChR and CD that participated in intermolecular interactions and identify γ-CD as a suitable host molecule for improving the hydro-solubulity of ChR. The structural insights would help to derive new derivatives of γ-CD with better host capacity.
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Affiliation(s)
- Pramod Kumar
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP 176061, India; Biotechnology division, CSIR-IHBT, Palampur, HP 176061, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Vijay Kumar Bhardwaj
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP 176061, India; Biotechnology division, CSIR-IHBT, Palampur, HP 176061, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Rituraj Purohit
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP 176061, India; Biotechnology division, CSIR-IHBT, Palampur, HP 176061, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad-201002, India.
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4
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El-Sayed DS, Tawfik EM, Elhusseiny AF, El-Dissouky A. A perception into binary and ternary copper (II) complexes: synthesis, characterization, DFT modeling, antimicrobial activity, protein binding screen, and amino acid interaction. BMC Chem 2023; 17:55. [PMID: 37316928 DOI: 10.1186/s13065-023-00962-x] [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: 01/17/2023] [Accepted: 05/25/2023] [Indexed: 06/16/2023] Open
Abstract
Ensuring healthy lives and promoting well-being for all at all ages is the third goal of the sustainable development plan, so it was necessary to identify the most important problems that threaten health in our world. The World Health Organization declared that antibiotic resistance is one of the uppermost global public health threats facing humanity and searching for new antibiotics is slow. This problem can be approached by improving available drugs to combat various bacterial threats. To circumvent bacterial resistance, three copper(II) complexes based on the pefloxacin drug were prepared and characterized using analytical, spectroscopic, and thermal techniques. The resulting data suggested the formation of one octahedral binary and two distorted square pyramidal ternary complexes. Fluorescence spectra results revealed the formation of a turn-on fluorophore for amino acid detection. Computational calculations investigated quantum and reactivity parameters. Molecular electrostatic potential profiles and noncovalent bond interaction-reduced density gradient analysis indicated the active sites on the complex surface. The complexes were subjected to six microbial species, where the octahedral binary complex provoked its antimicrobial potency in comparison with ternary complexes. The enhanced antimicrobial activity against gram-negative bacterium E-coli compared to gentamicin was exhibited by the three complexes. Docking simulation was performed based on the crystal structure of E. coli and S. pneumoniae receptors using 5I2D and 6O15 codes. The binary complex exhibited a potent fitness score with 5I2D (TBE = - 107 kcal/mol) while ternary complexes displayed the highest docked score of fitness with 6O15.
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Affiliation(s)
- Doaa S El-Sayed
- Chemistry Department, Faculty of Science, Alexandria University, 2 Bagdad Street, P.O. Box 2-Moharrem Beck, Alexandria, 21321, Egypt.
| | - Eman M Tawfik
- Chemistry Department, Faculty of Science, Alexandria University, 2 Bagdad Street, P.O. Box 2-Moharrem Beck, Alexandria, 21321, Egypt
| | - Amel F Elhusseiny
- Chemistry Department, Faculty of Science, Alexandria University, 2 Bagdad Street, P.O. Box 2-Moharrem Beck, Alexandria, 21321, Egypt
| | - Ali El-Dissouky
- Chemistry Department, Faculty of Science, Alexandria University, 2 Bagdad Street, P.O. Box 2-Moharrem Beck, Alexandria, 21321, Egypt
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5
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Structural insights, spectral, flourescence, Z-scan, C-H…O/N-H…O hydrogen bonding and AIM, RDG, ELF, LOL, FUKUI analysis, NLO activity of N-2(Methoxy phenyl) acetamide. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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6
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Garg U, Azim Y. Experimental and computational analyses of the cocrystal of Tetrahydrofuran-2,3,4,5-tetracarboxylic acid and urea. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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7
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Jana R, Ahmed SA, Seth D. Interaction between Cucurbit[7]uril and Bile Salts: An Isothermal Titration Calorimetry Study. ChemistrySelect 2022. [DOI: 10.1002/slct.202103800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Rabindranath Jana
- Department of Chemistry Indian Institute of Technology Patna Patna 801103 Bihar India
| | - Sayeed Ashique Ahmed
- Department of Chemistry Indian Institute of Technology Patna Patna 801103 Bihar India
| | - Debabrata Seth
- Department of Chemistry Indian Institute of Technology Patna Patna 801103 Bihar India
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8
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A DFT and molecular dynamics simulation study of single-walled carbon nanotube as a drug delivery system for few model nitrogen mustard drugs. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130877] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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9
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Intermolecular interactions in microhydrated ribonucleoside and deoxyribonucleoside: A computational study. COMPUT THEOR CHEM 2021. [DOI: 10.1016/j.comptc.2021.113422] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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10
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Venkataramanan NS. Electronic structure, stability, and cooperativity of chalcogen bonding in sulfur dioxide and hydrated sulfur dioxide clusters: a DFT study and wave functional analysis. Struct Chem 2021. [DOI: 10.1007/s11224-021-01827-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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11
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Garg U, Azim Y, Alam M. In acid-aminopyrimidine continuum: experimental and computational studies of furan tetracarboxylate-2-aminopyrimidinium salt. RSC Adv 2021; 11:21463-21474. [PMID: 35478783 PMCID: PMC9034213 DOI: 10.1039/d1ra01714d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 06/08/2021] [Indexed: 12/27/2022] Open
Abstract
Salts and cocrystals are the two important solid forms when a carboxylic acid crystallizes with an aminopyrimidine base such that the extent of proton transfer distinguishes between them. The ΔpKa value (pKa(base) − pKa(acid)) predicts whether the proton transfer will occur or not. However, the ΔpKa range, 0 < ΔpKa < 3, is elusive where the formation of cocrystal or salt cannot be predicted. The current study has been done to obtain a generalization in this elusive range with the Cambridge Structural Database (CSD). Based on the generalization, a novel salt (FTCA)−(2-AP)+ of furantetracarboxylic acid (FTCA) with 2-aminopyrimidine (2-AP) is obtained. The structural confirmation was done by single-crystal X-ray diffraction (SCXRD). Density functional theory (DFT) calculations were performed at the IEF-PCM-B3LYP-D3/6-311G(d,p) level to optimize the geometrical coordinates of salt for frontier molecular orbitals (FMOs) and molecular electrostatic potential (MESP). The geometrical parameters of most of the atoms of the optimized salt structure were comparable with SCXRD data. Additionally, results of other computational methods such as ab initio (Hartree–Fock; HF and second-order-Møller–Plesset perturbation; MP2) and semi-empirical were also compared with experimental results of the salt. Quantum theory of atoms in molecules (QTAIM), reduced density gradient (RDG), and natural bond orbital (NBO) analyses were done to calculate the strength and nature of non-covalent interactions present in the salt. Furthermore, Hirshfeld surface analysis, interaction energy calculations, and total energy frameworks were performed for qualitative and quantitative estimations of strong and weak intermolecular interactions. Generalization in the elusive ΔpKa range, experimental and computational studies of furan tetracarboxylate-2-aminopyrimidinium salt.![]()
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Affiliation(s)
- Utsav Garg
- Department of Applied Chemistry, Zakir Husain College of Engineering & Technology, Aligarh Muslim University Aligarh 202002 Uttar Pradesh India
| | - Yasser Azim
- Department of Applied Chemistry, Zakir Husain College of Engineering & Technology, Aligarh Muslim University Aligarh 202002 Uttar Pradesh India
| | - Mahboob Alam
- Division of Chemistry & Biotechnology, Dongguk University 123 Dongdae-ro Gyeongju Republic of Korea
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12
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A computational study on the complexation of bisbenzimidazolyl derivatives with cucurbituril and cyclohexylcucurbituril. J INCL PHENOM MACRO 2021. [DOI: 10.1007/s10847-021-01078-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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13
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Nikolova V, Velinova A, Dobrev S, Kircheva N, Angelova S, Dudev T. Host-Guest Complexation of Cucurbit[7]Uril and Cucurbit[8]Uril with the Antineoplastic and Multiple Sclerosis Agent Mitoxantrone (Novantrone). J Phys Chem A 2021; 125:536-542. [PMID: 33415972 DOI: 10.1021/acs.jpca.0c08544] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The nature of interactions between the neutral/protonated mitoxantrone and the cucurbit[n]uril (n = 7, 8) host system was analyzed by employing density functional theory calculations. A comparison between the inclusion complexes of CB[7] and CB[8] shows various subtle differences in the complexation thermodynamics, given as changes in the Gibbs energy. Doubly and quadruply charged mitoxantrone (MX) molecules spontaneously form complexes in a water solvent, which are modeled using the polarizable continuum model approach. Both CB[7] and CB[8] complexes are stable as the geometry of the cavity allows for electrostatic interactions between the charged MX arms and the rim of the CB cavity. CB[8] also forms a stable complex with two mitoxantrone molecules with their aromatic rings stacked inside the cavity. Both CB[7] and CB[8] show properties that can be utilized in drug delivery.
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Affiliation(s)
- Valya Nikolova
- Faculty of Chemistry and Pharmacy, Sofia University "St. Kl. Ohridski", 1164 Sofia, Bulgaria
| | - Anita Velinova
- Faculty of Chemistry and Pharmacy, Sofia University "St. Kl. Ohridski", 1164 Sofia, Bulgaria
| | - Stefan Dobrev
- Institute of Optical Materials and Technologies "Acad. J. Malinowski", Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Nikoleta Kircheva
- Institute of Optical Materials and Technologies "Acad. J. Malinowski", Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Silvia Angelova
- Institute of Optical Materials and Technologies "Acad. J. Malinowski", Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Todor Dudev
- Faculty of Chemistry and Pharmacy, Sofia University "St. Kl. Ohridski", 1164 Sofia, Bulgaria
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14
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Li F, Zheng Z, Xia S, Yu L. Synthesis, co-crystal structure, and DFT calculations of a multicomponent co-crystal constructed from 1H-benzotriazole and tetrafluoroterephthalic acid. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128480] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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15
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Yahiaoui K, Seridi L, Mansouri K. Temozolomide binding to Cucurbit[7]uril: QTAIM, NCI-RDG and NBO analyses. J INCL PHENOM MACRO 2020. [DOI: 10.1007/s10847-020-01027-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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16
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Xie L, Xiao N, Li L, Xie X, Li Y. Theoretical Insight into the Interaction between Chloramphenicol and Functional Monomer (Methacrylic Acid) in Molecularly Imprinted Polymers. Int J Mol Sci 2020; 21:ijms21114139. [PMID: 32532004 PMCID: PMC7312358 DOI: 10.3390/ijms21114139] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/06/2020] [Accepted: 06/08/2020] [Indexed: 12/14/2022] Open
Abstract
Molecular imprinting technology is a promising method for detecting chloramphenicol (CAP), a broad-spectrum antibiotic with potential toxicity to humans, in animal-derived foods. This work aimed to investigate the interactions between the CAP as a template and functional monomers required for synthesizing efficient molecularly imprinted polymers for recognition and isolation of CAP based on density functional theory. The most suitable monomer, methacrylic acid (MAA), was determined based on interaction energies and Gibbs free energy changes. Further, the reaction sites of CAP and MAA was predicted through the frontier molecular orbitals and molecular electrostatic potentials. Atoms in molecules topology analysis and non-covalent interactions reduced density gradient were applied to investigate different types of non-covalent and inter-atomic interactions. The simulation results showed that CAP was the main electron donor, while MAA was the main electron acceptor. Moreover, the CAP–MAA complex simultaneously involved N-H···O and C=O···H double hydrogen bonds, where the strength of the latter was greater than that of the former. The existence of hydrogen bonds was also confirmed by theoretical and experimental hydrogen nuclear magnetic resonance and Fourier transform infrared spectroscopic analyses. This research can act as an important reference for intermolecular interactions and provide strong theoretical guidance regarding CAP in the synthesis of molecularly imprinted polymers.
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Affiliation(s)
| | | | - Lu Li
- Correspondence: ; Tel.: +86-13711240878
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17
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Khorrampour R, Raissi H, Shaki H, Morsali A, Hashemzadeh H. The scrutinised DFT and MD studies on the adsorption of D-penicillamine drug on γ-Fe 2O 3 nanoparticle as a highly efficient carrier. MOLECULAR SIMULATION 2020. [DOI: 10.1080/08927022.2020.1716979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
| | - Heidar Raissi
- Chemistry Department, University of Birjand, Birjand, Iran
| | - Hosien Shaki
- Chemistry Department, Payame Noor University, Mashhad, Iran
| | - Ali Morsali
- Chemistry Department, Mashhad Branch, Islamic Azad University, Mashhad, Iran
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18
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Unraveling the binding nature of hexane with quinone functionalized pillar[5]quinone: a computational study. J INCL PHENOM MACRO 2019. [DOI: 10.1007/s10847-019-00945-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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19
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Anion-binding properties of π-electron deficient cavity in tetraoxacalix[2]arene[2]triazine by a computational study. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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20
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Suvitha A, Venkataramanan NS, Sahara R, Kawazoe Y. A theoretical exploration of the intermolecular interactions between resveratrol and water: a DFT and AIM analysis. J Mol Model 2019; 25:56. [DOI: 10.1007/s00894-019-3941-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 01/24/2019] [Indexed: 12/27/2022]
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21
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Venkataramanan NS, Suvitha A, Sahara R. Structure, stability, and nature of bonding between high energy water clusters confined inside cucurbituril: A computational study. COMPUT THEOR CHEM 2019. [DOI: 10.1016/j.comptc.2018.12.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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22
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Oliveira OVD, Costa GDC, Costa LT. Encapsulation of the Sulfur Compounds by Cucurbit[7]uril: A Quantum Chemistry Study. J Phys Chem B 2018; 122:12107-12113. [PMID: 30452266 DOI: 10.1021/acs.jpcb.8b09419] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Benzothiophene (BT) and dibenzothiophene (DT) are the most important contaminants in the petroleum derivatives responsible for serious environmental and health problems. Therefore, we have investigated the absorption of these compounds for the first time by considering cucurbit[7]uril (CB[7]) as the host molecule and using the theoretical levels of density functional theory//B3LYP-D3/6-31G(d). BT and DT absorbed into CB[7] do not undergo a significant structural change in the CB[7] structure. The energy gap of the S-compounds@CB[7] in water and hexane solvents was approximately 5 eV, and this large value implies that the complexes have high chemical stability. Moreover, the absorption of the BT and DT into CB[7] in the water and hexane solvents is a favorable process, whereas the lowest binding energy was observed between the dibenzothiophene and CB[7] in the DT@CB[7] complex. The solvation enthalpy shows a preferential solvation of the complexes in water than in hexane solvent. This trend is confirmed by the AIM analysis that shows the highest stability for the DT@CB[7] system with the contribution of cooperative hydrogen bonding. The transfer free energy of S-compounds@CB[7] complexes from hexane to water are -66.12 and -59.56 kcal/mol for BT@CB[7] and DT@CB[7], respectively, implying the spontaneous transference of these complexes from hexane to water solvent. Overall, our results show that the cucurbiturils can be a new class of host molecules to be used in the removal of S-compounds from petroleum derivatives. Finally, a schematic flow diagram of the desulfurization process by cucurbiturils was proposed.
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Affiliation(s)
- Osmair Vital de Oliveira
- Instituto Federal de Educação Ciência e Tecnologia de São Paulo, campus Catanduva , CEP: 29106-010 , Catanduva, São Paulo 15808-305 , Brazil
| | - Gabriela de Carvalho Costa
- Instituto de Química, Universidade Federal Fluminense - Outeiro de São João Batista , s/n CEP:24020-141 , Niterói, Rio de Janeiro 24210-000 , Brazil
| | - Luciano T Costa
- Instituto de Química, Universidade Federal Fluminense - Outeiro de São João Batista , s/n CEP:24020-141 , Niterói, Rio de Janeiro 24210-000 , Brazil
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23
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A joint MD/QM study on the possibility of alkaloids detection by cucurbiturils and graphene oxide-cucurbituril composites. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.10.092] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Deciphering the nature of interactions in nandrolone/testosterone encapsulated cucurbituril complexes: a computational study. J INCL PHENOM MACRO 2018. [DOI: 10.1007/s10847-018-0869-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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25
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Interaction between carboplatin and cucurbit[7]uril studied by means of multinuclear NMR spectroscopy and DFT calculations. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.02.108] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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26
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Venkataramanan NS, Suvitha A, Kawazoe Y. Unravelling the nature of binding of cubane and substituted cubanes within cucurbiturils: A DFT and NCI study. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.03.071] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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27
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Satpathi S, Singh RK, Mukherjee A, Hazra P. Controlling anticancer drug mediated G-quadruplex formation and stabilization by a molecular container. Phys Chem Chem Phys 2018; 20:7808-7818. [PMID: 29504620 DOI: 10.1039/c8cp00325d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Controlling of ligand mediated G-quadruplex DNA (GQ-DNA) formation and stabilization is an important and challenging aspect due to its active involvement in many biologically important processes such as DNA replication, transcription, etc. Here, we have demonstrated that topotecan (TPT), a potential anticancer drug, can instigate the formation and stabilization of GQ-DNA (H24 → GQ-DNA) in the absence of Na+/K+ ions via circular dichroism, fluorescence, NMR, UV melting and molecular dynamics (MD) simulation studies. The primary binding mode of TPT to GQ was found to be stacking at the terminal rather than binding to the groove. We have also reverted this conformational transition (GQ-DNA → H24) using a molecular container, cucurbit[7]uril (CB7), by means of the translocation of the drug (TPT) from GQ-DNA to its nanocavity. Importantly, we have carried out the detection of these conformational transitions using the fluorescence color switch of the drug, which is more direct and simple than some of the other methods that involve sophisticated and complex detection techniques.
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Affiliation(s)
- Sagar Satpathi
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr Homi Bhabha Road, Pashan, Pune 411008, India.
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28
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Senthilnathan D, Solomon RV, Kiruthika S, Venuvanalingam P, Sundararajan M. Are cucurbiturils better drug carriers for bent metallocenes? Insights from theory. J Biol Inorg Chem 2018; 23:413-423. [PMID: 29502216 DOI: 10.1007/s00775-018-1547-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 02/23/2018] [Indexed: 02/06/2023]
Abstract
Bent metallocenes (BM) have anti-tumor properties but they face a serious drug efficacy problem due to poor aqueous solubility and rapid hydrolysis under physiological conditions. These two problems can be fixed by encapsulating them in host molecules such as cyclodextrin (CD), cucurbituril (CB) etc. Experimentally, CD-BM, CB-BM host-guest complexes have been investigated to check the efficiency of the drug delivery and efficiency of the encapsulated drug. CB has been reported to be a better host than CD but the reasons for this has not been figured out. This can be done by finding out the mechanism of binding and the nature of the binding forces in both the inclusion complexes. This is exactly done here by performing a DFT study at BP86/TZP level on CB-BM host-guest systems. For comparison CD-BM with β-cyclodextrin as host have been studied. Four BMs (Cp2MCl2, M=Ti, V, Nb, Mo) and their corresponding cations (Cp2MCl+, Cp2M2+) are chosen as guests and they are encapsulated into cucurbit-[6]-uril (CB[6]) and cucurbit-[7]-uril(CB[7]) host systems. Computations reveal that CB[7] accommodates well the BMs over CB[6] due to their larger cavity size and also CB[7] is found to be a better host than β-cyclodextrin. BMs enter vertically rather than horizontally into the CB cavity. The reversible binding of BMs within CB[7] is controlled by various non-bonding interactions and mainly by hydrogen bonding between the portal oxygen atoms and Cp protons as revealed by QTAIM analysis. On the other hand, the interaction between the wall nitrogen atoms in CB[7] and chlorine atoms attached to the metal in BM strengthens the M-Cl bonds that prevents rapid hydrolysis of M-Cl and M-Cp bonds saving the drug. Comparatively, BMs experience less electrostatic attraction and more Pauli repulsion within β-cyclodextrin cavity and this affects the drug binding with CD. This makes β-cyclodextrin a less suitable drug carrier for BMs than CBs. Among the four BMs, niobocene binds strongly and titanocene binds weakly with CBs. EDA clearly shows that all the interactions between the guest and host are non-covalent in nature and electrostatic interactions outperform high-repulsion resulting in stable complexes. Cations form stronger complexes than neutral BMs. FMO analysis reveals that neutral BMs are less reactive compared to their cations and complexes are more reactive in CB[6] environment due to excess strain. QTAIM analysis helps to bring out the newer insights in these types of host-guest systems.
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Affiliation(s)
- Dhurairajan Senthilnathan
- Center for Computational Chemistry, CRD, PRIST University, Vallam, Thanjavur, Tamilnadu, 613403, India.
| | - Rajadurai Vijay Solomon
- Department of Chemistry, Madras Christian College (Autonomous), Tambaram East, Chennai, 600 059, India
| | - Shanmugam Kiruthika
- Theoretical and Computational Chemistry Laboratory, School of Chemistry, Bharathidasan University, Tiruchirappalli, 620 024, India
| | - Ponnambalam Venuvanalingam
- Theoretical and Computational Chemistry Laboratory, School of Chemistry, Bharathidasan University, Tiruchirappalli, 620 024, India
| | - Mahesh Sundararajan
- Theoretical Chemistry Section, Bhabha Atomic Research Centre, Mumbai, 400 085, India
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29
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Venkataramanan NS, Suvitha A. Nature of bonding and cooperativity in linear DMSO clusters: A DFT, AIM and NCI analysis. J Mol Graph Model 2018. [PMID: 29524753 DOI: 10.1016/j.jmgm.2018.02.010] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
This study aims to cast light on the nature of interactions and cooperativity that exists in linear dimethyl sulfoxide (DMSO) clusters using dispersion corrected density functional theory. In the linear DMSO, DMSO molecules in the middle of the clusters are bound strongly than at the terminal. The plot of the total binding energy of the clusters vs the cluster size and mean polarizabilities vs cluster size shows an excellent linearity demonstrating the presence of cooperativity effect. The computed incremental binding energy of the clusters remains nearly constant, implying that DMSO addition at the terminal site can happen to form an infinite chain. In the linear clusters, two σ-hole at the terminal DMSO molecules were found and the value on it was found to increase with the increase in cluster size. The quantum theory of atoms in molecules topography shows the existence of hydrogen and SO⋯S type in linear tetramer and larger clusters. In the dimer and trimer SO⋯OS type of interaction exists. In 2D non-covalent interactions plot, additional peaks in the regions which contribute to the stabilization of the clusters were observed and it splits in the trimer and intensifies in the larger clusters. In the trimer and larger clusters in addition to the blue patches due to hydrogen bonds, additional, light blue patches were seen between the hydrogen atom of the methyl groups and the sulphur atom of the nearby DMSO molecule. Thus, in addition to the strong H-bonds, strong electrostatic interactions between the sulphur atom and methyl hydrogens exists in the linear clusters.
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Affiliation(s)
| | - Ambigapathy Suvitha
- Department of Chemistry, School of Chemical and Biotechnology (SCBT), SASTRA Deemed University, Thanjavur, 613 401, India
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30
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Density functional theory study on the dihydrogen bond cooperativity in the growth behavior of dimethyl sulfoxide clusters. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2017.11.062] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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31
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Intermolecular interaction in nucleobases and dimethyl sulfoxide/water molecules: A DFT, NBO, AIM and NCI analysis. J Mol Graph Model 2017; 78:48-60. [DOI: 10.1016/j.jmgm.2017.09.022] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 09/27/2017] [Accepted: 09/28/2017] [Indexed: 01/05/2023]
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32
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Venkataramanan NS, Suvitha A, Vijayaraghavan A, Thamotharan S. Investigation of inclusion complexation of acetaminophen with pillar [5]arene: UV–Vis, NMR and quantum chemical study. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2017.06.095] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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33
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Mohan M, Suzuki T, Nair AK, Pillai S, Warrier KGK, Hareesh US, Nair BN, Gale JD. Surface modification induced enhanced CO2 sorption in cucurbit[6]uril, an organic porous material. Phys Chem Chem Phys 2017; 19:25564-25573. [DOI: 10.1039/c7cp03866f] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Theoretical and experimental studies on CO2 sorption of the organic macrocycle cucurbit[6]uril (CB[6]).
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Affiliation(s)
- Midhun Mohan
- Functional Materials
- Material Science and Technology Division
- CSIR-National Institute for Interdisciplinary Science and Technology
- Trivandrum-695 019
- India
| | - T. Suzuki
- R&D Center
- Noritake Co. Ltd
- Miyoshi
- Japan
| | - Akhil K. Nair
- Functional Materials
- Material Science and Technology Division
- CSIR-National Institute for Interdisciplinary Science and Technology
- Trivandrum-695 019
- India
| | - Saju Pillai
- Functional Materials
- Material Science and Technology Division
- CSIR-National Institute for Interdisciplinary Science and Technology
- Trivandrum-695 019
- India
| | - K. G. K. Warrier
- Functional Materials
- Material Science and Technology Division
- CSIR-National Institute for Interdisciplinary Science and Technology
- Trivandrum-695 019
- India
| | - U. S. Hareesh
- Functional Materials
- Material Science and Technology Division
- CSIR-National Institute for Interdisciplinary Science and Technology
- Trivandrum-695 019
- India
| | - Balagopal N. Nair
- R&D Center
- Noritake Co. Ltd
- Miyoshi
- Japan
- Curtin Institute for Computation
| | - J. D. Gale
- Curtin Institute for Computation
- Department of Chemistry
- Curtin University
- Perth
- Australia
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