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Alcolea Palafox M, Belskaya NP, Todorov LT, Kostova IP. Structural Study of a La(III) Complex of a 1,2,3-Triazole Ligand with Antioxidant Activity. Antioxidants (Basel) 2023; 12:1872. [PMID: 37891952 PMCID: PMC10604163 DOI: 10.3390/antiox12101872] [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: 09/20/2023] [Revised: 10/10/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
The 1,2,3-triazole derivative 2-(4-chlorophenyl)-5-(pyrrolidin-1-yl)-2H-1,2,3-triazole-4-carboxylic acid with potential anticancer activity was used as a ligand in complex formation with the lanthanum(III) ion. The molecular structure and vibrational spectra of the complex were optimized at three DFT levels, and the scaled IR and Raman spectra were compared to the experimental ones. Several scaling procedures were used. Through a detailed analysis, the structure predicted for the newly synthetized La(III) complex was confirmed by the good accordance of the calculated/experimental IR and Raman spectra. The best DFT method appeared to be M06-2X with the Lanl2mb basis set, followed closely by Lanl2dz. The effect of the lanthanide atom on the molecular structure and atomic charge distribution of the triazole ring was evaluated. The potential free radical scavenging activity of both the ligand and the complex was investigated in several radical-generating model systems. The potential mechanisms of antioxidant action (hydrogen atom transfer (HAT) and single-electron transfer (SET)) were elucidated.
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Affiliation(s)
- Mauricio Alcolea Palafox
- Department of Physical Chemistry, Faculty of Chemical Sciences, Complutense University, 28040 Madrid, Spain
| | - Nataliya P. Belskaya
- Department of Technology for Organic Synthesis, Ural Federal University, 19 Mira Str., Yekaterinburg 620012, Russia;
| | - Lozan T. Todorov
- Department of Chemistry, Faculty of Pharmacy, Medical University—Sofia, 2 Dunav Str., 1000 Sofia, Bulgaria;
| | - Irena P. Kostova
- Department of Chemistry, Faculty of Pharmacy, Medical University—Sofia, 2 Dunav Str., 1000 Sofia, Bulgaria;
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Wang L, Zhang P, Geng Y, Zhu Z, Yuan S. Harmonic Vibrational Frequency Simulation of Pharmaceutical Molecules via a Novel Multi-Molecular Fragment Interception Method. Molecules 2023; 28:4638. [PMID: 37375193 DOI: 10.3390/molecules28124638] [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: 05/16/2023] [Revised: 06/05/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
By means of a computational method based on Density Functional Theory (DFT), using commercially available software, a novel method for simulating equilibrium geometry harmonic vibrational frequencies is proposed. Finasteride, Lamivudine, and Repaglinide were selected as model molecules to study the adaptability of the new method. Three molecular models, namely the single-molecular, central-molecular, and multi-molecular fragment models, were constructed and calculated by Generalized Gradient Approximations (GGAs) with the PBE functional via the Material Studio 8.0 program. Theoretical vibrational frequencies were assigned and compared to the corresponding experimental data. The results indicated that the traditional single-molecular calculation and scaled spectra with scale factor exhibited the worst similarity for all three pharmaceutical molecules among the three models. Furthermore, the central-molecular model with a configuration closer to the empirical structure resulted in a reduction of mean absolute error (MAE) and root mean squared error (RMSE) in all three pharmaceutics, including the hydrogen-bonded functional groups. However, the improvement in computational accuracy for different drug molecules using the central-molecular model for vibrational frequency calculation was unstable. Whereas, the new multi-molecular fragment interception method showed the best agreement with experimental results, exhibiting MAE and RMSE values of 8.21 cm-1 and 18.35 cm-1 for Finasteride, 15.95 cm-1 and 26.46 cm-1 for Lamivudine, and 12.10 cm-1 and 25.82 cm-1 for Repaglinide. Additionally, this work provides comprehensive vibrational frequency calculations and assignments for Finasteride, Lamivudine, and Repaglinide, which have never been thoroughly investigated in previous research.
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Affiliation(s)
- Linjie Wang
- School of Chemical Engineering, Shandong Institute of Petroleum and Chemical Technology, Dongying 257061, China
| | - Pengtu Zhang
- School of Chemical Engineering, Shandong Institute of Petroleum and Chemical Technology, Dongying 257061, China
| | - Yali Geng
- School of Chemical Engineering, Shandong Institute of Petroleum and Chemical Technology, Dongying 257061, China
| | - Zaisheng Zhu
- School of Chemical Engineering, Shandong Institute of Petroleum and Chemical Technology, Dongying 257061, China
| | - Shiling Yuan
- School of Chemical Engineering, Shandong Institute of Petroleum and Chemical Technology, Dongying 257061, China
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250199, China
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Karpagavalli K, Daisy Magdaline J, Chithambarathanu T. Vibrational frequency Analysis, DFT and in Vitro Fungicidal Activity Studies of Biphenyl-4-Carboxylic Acid, 2,4-Difluorobiphenyl and 4-Acetylbiphenyl- A Comparative Study. Polycycl Aromat Compd 2023. [DOI: 10.1080/10406638.2023.2169474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Affiliation(s)
- K. Karpagavalli
- Research Department of Physics, Rani Anna Government College for Women, Tirunelveli, Tamil Nadu, India
- Department of Physics, Manonmaniam Sundaranar University, Tirunelveli, Tamil Nadu, India
| | - J. Daisy Magdaline
- Research Department of Physics, Rani Anna Government College for Women, Tirunelveli, Tamil Nadu, India
- Department of Physics, Manonmaniam Sundaranar University, Tirunelveli, Tamil Nadu, India
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Kavitha E, Ramarajan D, Rakić A, Dimić D, Sudha S, Nirmala PN. Structural, spectroscopic, quantum chemical, and molecular docking investigation of (E)-N'-(2,5-dimethoxybenzylidene)picolinohydrazide. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.132259] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Rodrigues A, Silva S, Oliveira M, de Oliveira G, Novais A, de Paula G, Souza D, Belo E, Gester R, Andrade-Filho T. Prediction of electronic and vibrational properties of poly (hexamethylene biguanide) hydrochloride: A combined theoretical and experimental investigation. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.131176] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Belh SJ, Ghosh G, Greer A. Surface-Radical Mobility Test by Self-Sorted Recombination: Symmetrical Product upon Recombination (SPR). J Phys Chem B 2021; 125:4212-4220. [PMID: 33856798 DOI: 10.1021/acs.jpcb.1c01099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We describe here a study of the mobility of the alkoxy radical on a surface by detection of its recombination product. A novel method called symmetrical product recombination (SRP) uses an unsymmetrical peroxide that upon sensitized homolysis recombines to a symmetrical product [R'OOR → R'O•↑ + •OR → ROOR]. This allows for self-sorting of the radical to enhance the recombination path to a symmetrical product, which has been used to deduce surface migratory aptitude. SPR also provides a new opportunity for mechanistic studies of interfacial radicals, including monitoring competition between radical recombination versus surface hydrogen abstraction. This is an approach that might work for other surface-borne radicals on natural and artificial particles.
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Affiliation(s)
- Sarah J Belh
- Department of Chemistry, Brooklyn College, 2900 Bedford Avenue, Brooklyn, New York 11210, United States.,Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
| | - Goutam Ghosh
- Department of Chemistry, Brooklyn College, 2900 Bedford Avenue, Brooklyn, New York 11210, United States.,Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
| | - Alexander Greer
- Department of Chemistry, Brooklyn College, 2900 Bedford Avenue, Brooklyn, New York 11210, United States.,Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
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Conformations, molecular structure, and N–H⋯O hydrogen bond strength in 4-Alkylamino-3-penten-2-ones. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127440] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Palafox MA, Chalanchi SM, Isasi J, Premkumar R, Franklin Benial AM, Rastogi VK. Effect of bromine atom on the different tautomeric forms of microhydrated 5-bromouracil, in the DNA:RNA microhelix and in the interaction with human proteins. J Biomol Struct Dyn 2020; 38:5443-5463. [DOI: 10.1080/07391102.2019.1704878] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- M. Alcolea Palafox
- Facultad de Ciencias Químicas, Departamento de Química-Fisica, Universidad Complutense de Madrid, Madrid, Spain
| | - S. M. Chalanchi
- Department of Chemistry, University of Sistan and Baluchestan, Zahedan, Iran
| | - J. Isasi
- Facultad de Ciencias Químicas, Departamento de Química Inorgánica, Universidad Complutense de Madrid, Madrid, Spain
| | - R. Premkumar
- PG and Research Department of Physics, N.M.S.S.V.N. College, Madurai, Tamil Nadu, India
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Shamala D, Shivashankar K, Chandra, Mahendra M. Zinc chloride catalyzed multicomponent synthesis of pyrazolopyridocoumarin scaffolds. J CHEM SCI 2019. [DOI: 10.1007/s12039-019-1610-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Alcolea Palafox M. Effect of the sulfur atom on S2 and S4 positions of the uracil ring in different DNA:RNA hybrid microhelixes with three nucleotide base pairs. Biopolymers 2019; 110:e23247. [PMID: 30676643 DOI: 10.1002/bip.23247] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 11/03/2018] [Accepted: 11/07/2018] [Indexed: 02/06/2023]
Abstract
The effect of the sulphur atom on the uracil ring was analyzed in different DNA:RNA microhelixes with three nucleotide base-pairs, including uridine, 2-thiouridine, 4-thiouridine, 2,4-dithiouridine, cytidine, adenosine and guanosine. Distinct backbone and helical parameters were optimized at different density functional (DFT) levels. The Watson-Crick pair with 2-thiouridine appears weaker than with uridine, but its interaction with water molecules appears easier. Two types of microhelixes were found, depending on the H-bond of H2' hydroxyl atom: A-type appears with the ribose ring in 3 E-envelope C3' -endo, and B-type in 2 E-envelope C2' -endo. B-type is less common but it is more stable and with higher dipole-moment. The sulphur atoms significantly increase the dipole-moment of the microhelix, as well as the rise and propeller twist parameters. Simulations with four Na atoms H-bonded to the phosphate groups, and further hydration with explicit water molecules were carried out. A re-definition of the numerical value calculation of several base-pair and base-stacking parameters is suggested.
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Affiliation(s)
- Mauricio Alcolea Palafox
- Departamento de Química-Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid, Spain
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Paul S, Karar M, Das B, Mallick A, Majumdar T. Theory after experiment on sensing mechanism of a newly developed sensor molecule: Converging or diverging? Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.10.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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Exploring the effect of confinement on water clusters in carbon nanotubes. J Mol Model 2017; 23:133. [PMID: 28341994 DOI: 10.1007/s00894-017-3299-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Accepted: 02/27/2017] [Indexed: 10/19/2022]
Abstract
Using armchair-type single-walled carbon nanotubes (SWCNTs) of different sizes as model compounds for lignite, the effect of water molecule confinement on the water-holding capacity of lignite pores was investigated. Results indicated that the water-holding capacity of pores with diameters of <10 nm was eight times larger than that of pores with diameters of 100 nm. The configuration of the cluster of water molecules in each SWCNT and the binding energy between each SWCNT and the water molecules within it were calculated by means of density functional theory using a hybrid functional: M06-2X/6-311+G**, 6-31G*. The results prove that the configurations of the water molecules in the SWCNTs are very different to their configuration in the unconfined state. In vacuum, the cluster of three water molecules adopted a trimer configuration, while they presented a linear configuration in the 6.78 Å SWCNT. Similarly, in vacuum, the cluster of five water molecules formed a five-membered ring, while they favored a linear configuration in the 6.78 Å SWCNT, a zigzag configuration in the 8.14 Å SWCNT, and a trimer + 1 + 1 configuration (i.e., a trimer plus two isolated water molecules) in the 9.49 Å, 10.85 Å, and 13.75 Å SWCNTs. There was found to be a degree of competition between the coupling energy of the water molecules with the SWCNT and the hydrogen bonding among the water molecules. When the diameter of the SWCNT was >1 nm, the hydrogen bonding among the water molecules dominated, while the coupling energy of the water molecules with the SWCNT amounted to only 30-40% of the total interaction energy of the water molecules. Graphical Abstract Computed equilibrium structures of five water molecules confined in SWCNTs with diameters of 6.78 Å, 8.14 Å, 9.49 Å, 10.85 Å, and 13.75 Å, and in vacuum.
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Delgado Espinosa ZY, Saeed A, Mahmood S, Echeverría GA, Piro OE, Erben MF. The effect of chalcogen substitution on the structure and spectroscopy of 4,7-dimethyl-2H-chromen-2-one/thione analogues. NEW J CHEM 2017. [DOI: 10.1039/c7nj01311f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The structural and spectroscopic properties of the 1-benzopyran-2-one/thione moiety.
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Affiliation(s)
- Zuly Yuliana Delgado Espinosa
- CEQUINOR (UNLP, CONICET-CCT La Plata)
- Departamento de Química
- Facultad de Ciencias Exactas
- Universidad Nacional de La Plata
- La Plata (1900)
| | - Aamer Saeed
- Department of Chemistry
- Quaid-I-Azam University
- Islamabad 45320
- Pakistan
| | - Shamsul Mahmood
- Department of Chemistry
- Quaid-I-Azam University
- Islamabad 45320
- Pakistan
| | - Gustavo A. Echeverría
- IFLP (CONICET, CCT-La Plata) Instituto de Física La Plata
- Departamento de Física
- Facultad de Ciencias Exactas
- Universidad Nacional de La Plata
- La Plata (1900)
| | - Oscar E. Piro
- IFLP (CONICET, CCT-La Plata) Instituto de Física La Plata
- Departamento de Física
- Facultad de Ciencias Exactas
- Universidad Nacional de La Plata
- La Plata (1900)
| | - Mauricio F. Erben
- CEQUINOR (UNLP, CONICET-CCT La Plata)
- Departamento de Química
- Facultad de Ciencias Exactas
- Universidad Nacional de La Plata
- La Plata (1900)
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Shamala D, Shivashankar K. Synthesis of 4-phenyloxazinones via DBU-catalyzed cleavage of 4-bromomethylcoumarins. SYNTHETIC COMMUN 2016. [DOI: 10.1080/00397911.2016.1252045] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Devadas Shamala
- P.G. Department of Chemistry, Central College Campus, Bangalore University, Bangalore, Karnataka, India
| | - Kalegowda Shivashankar
- P.G. Department of Chemistry, Central College Campus, Bangalore University, Bangalore, Karnataka, India
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Shamala D, Shivashankar K. Synthesis of pyridazinones via molecular-iodine-mediated cleavage of 4-bromomethylcoumarin precursors. SYNTHETIC COMMUN 2016. [DOI: 10.1080/00397911.2016.1223310] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Devadas Shamala
- P. G. Department of Chemistry, Central College Campus, Bangalore University, Bangalore, Karnataka, India
| | - Kalegowda Shivashankar
- P. G. Department of Chemistry, Central College Campus, Bangalore University, Bangalore, Karnataka, India
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Vibrational assignments, spectroscopic investigation (FT-IR and FT-Raman), NBO, MEP, HOMO‒LUMO analysis and intermolecular hydrogen bonding interactions of 7-fluoroisatin, 7-bromoisatin and 1-methylisatin ‒ A comparative study. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2015.08.033] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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