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Elangovan N, Arumugam N, Almansour AI, Mathew S, Djearamane S, Wong LS, Kayarohanam S. Synthesis, solvent role, absorption and emission studies of cytosine derivative. Heliyon 2024; 10:e28623. [PMID: 38590870 PMCID: PMC11000011 DOI: 10.1016/j.heliyon.2024.e28623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 03/19/2024] [Accepted: 03/21/2024] [Indexed: 04/10/2024] Open
Abstract
The (E)-4-((4-hydroxy-3-methoxy-5-nitrobenzylidene) amino) pyrimidin-2(1H)-one (C5NV) was synthesized from cytosine and 5-nitrovanilline by simple straightforward condensation reaction. The structural characteristics of the compound was determined and optimized by WB97XD/cc-pVDZ basis set. The vibrational frequencies were computed and subsequently compared to the experimental frequencies. We investiated the electronic properties of the synthesized compound in gas and solvent phases using the time-dependent density functional theory (TD-DFT) approach, and compared them to experimental values. The fluorescence study showed three different wavelengths indicating the nature of the optical material properties. Frontier molecular orbital (FMO) and molecular electrostatic potential (MEP) analyses were conducted for the title compound, and electron localized functions (ELF) and localized orbital locators (LOL) were used to identify the orbital positions of localized and delocalized atoms. Non-covalent interactions (H-bond interactions) were investigated using reduced density gradients (RDGs). The objective of the study was to determine the physical, chemical, and biological properties of the C5NV. The molecular docking study was conducted between C5NV and 2XNF protein, its lowest binding energy score is -7.92 kcal/mol.
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Affiliation(s)
- N. Elangovan
- Research Centre for Computational and Theoretical Chemistry, Anjalam, 621208, Musiri, Tiruchirappalli, Tamilnadu, India
| | - Natarajan Arumugam
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Abdulrahman I. Almansour
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Shanty Mathew
- Department of Chemistry, St. Joseph's College Research Center, Shanthinagar, 560027, Bangalore, India
| | - Sinouvassane Djearamane
- Department of Allied Health Sciences, Faculty of Science, Universiti Tunku Abdul Rahman, Jalan Universiti, Bandar Barat, Kampar, 31900, Malaysia
- Biomedical Research Unit and Lab Animal Research Centre, Saveetha Dental College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, 602 105, India
| | - Ling Shing Wong
- Faculty of Health and Life Sciences, INTI International University, Nilai, 71800, Malaysia
| | - Saminathan Kayarohanam
- Faculty of Bioeconomics and Health Sciences, University Geomatika Malaysia, Kuala Lumpur, 54200, Malaysia
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Slimani Y, Boukaoud A, Chiba Y, Sebbar D, Ammar MA, Ayad A. Exploration of electronic and vibrational properties of sulfanilic acid through periodic and non-periodic DFT calculations. J Mol Model 2024; 30:121. [PMID: 38570393 DOI: 10.1007/s00894-024-05911-6] [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: 03/04/2024] [Accepted: 03/22/2024] [Indexed: 04/05/2024]
Abstract
CONTEXT The electronic, discrete water solvation, and vibrational properties of zwitterionic sulfanilic acid were thoroughly investigated using periodic and non-periodic DFT approaches. The periodic-DFT results, obtained by employing the PBE-TS functional (Perdew-Burke-Ernzerhof (PBE) functional with the Tkatchenko and Scheffler (TS) dispersion correction) were first presented in order to analyze the band structures of the studied crystal. An attentive reading of the predicted band structures has shown three lowest gap energies calculated at 4.23, 4.24, and 4.29 eV arising from the Γ→Γ, Γ→Z, and Γ→S transitions, respectively. Then, non-periodic calculations were carried out, at the B3LYP-D3 level of theory (B3LYP functional with the D3 Grimme dispersion correction) in order to optimize the sulfanilic acid-(H2O)10 complex. Starting from the optimized structure, non-covalent interaction calculations were performed and the H-bonding, van der Waals, and steric effect interactions were identified. Finally, the PBE-TS calculations were strengthened by conducting anharmonic B3LYP-D3 calculations in order to achieve a complete decryption of the experimental IR spectrum of sulfanilic acid. The spectral analysis is not limited only to the interpretation of both the NH/CH stretching and fingerprint regions but also extended to the 1800-2600 cm-1 region, which is characterized by a strong anharmonic effect. In the latter wavenumber region, the large experimental IR band centered at 1937 cm-1 is reproduced theoretically employing the anharmonic B3LYP-D3 calculations. The similarity of this band with those usually considered as a fingerprint of zwitterionic amino acids is observed, and its origin is elucidated theoretically. In the vibrational spectroscopy field, the calculations presented in this study are probably the most appropriate for achieving vast analysis and accurate assignments of vibrational spectra of hydrogen bonding compounds recorded in the solid state. METHOD The periodic and non-periodic calculations were conducted within the Density Functional Theory (DFT) using the Generalized Gradient Approximation (GGA) at the PBE-TS level of theory and B3LYP-D3 functional with the 6-311++G(d,p) basis set, respectively. The PBE-TS and B3LYP-D3/6-311++G(d,p) calculations were performed using the CASTEP and Gaussian 09 programs, respectively. In addition, The non-covalent interactions were calculated by the Multiwfn 3.8 software. The obtained results for different calculations were visualized by employing the visualization tools in Materials Studio, GaussView, VMD, and Gnuplot programs.
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Affiliation(s)
- Yasmine Slimani
- Laboratory of Physics of Experimental Techniques and Their Applications, University of Medea, 26000, Medea, Algeria
| | - Abdelali Boukaoud
- Laboratory of Physics of Experimental Techniques and Their Applications, University of Medea, 26000, Medea, Algeria.
| | - Younes Chiba
- Renewable Energy and Materials Laboratory, Mechanical Engineering Department, University of Medea, 26000, Medea, Algeria
| | - Djamel Sebbar
- Laboratory of Physics of Experimental Techniques and Their Applications, University of Medea, 26000, Medea, Algeria
| | - Mohammed Ahmed Ammar
- Laboratory of Physics of Experimental Techniques and Their Applications, University of Medea, 26000, Medea, Algeria
| | - Abdelhak Ayad
- Département de Pharmacie, Faculté de Médecine, Université Salah Boubnider Constantine 3, Nouvelle ville Ali Mendjeli, 25005, Constantine, Algeria
- Laboratoire Microstructures et Défauts dans les Matériaux, Univeristé Frères Mentouri Constantine 1, Route Ain El Bey, 25017, Constantine, Algeria
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Gupta PO, Sharma SJ, Sekar N. Theoretical investigation of substitution effect on the sixth and seventh positions of coumarin derivatives. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 304:123373. [PMID: 37708758 DOI: 10.1016/j.saa.2023.123373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 08/27/2023] [Accepted: 09/06/2023] [Indexed: 09/16/2023]
Abstract
The linear and non-linear optical properties of 6-donor and 7-donor substituted coumarins were compared using density functional theory (DFT) and time-dependent-DFT (TD-DFT). Charge transfer characteristics were investigated through natural bond order analysis, frontier molecular orbital, and molecular electrostatic potential plots. TD-DFT results suggested that the 6-donor substituted coumarins (PS1, PS3, and PS5) showed red-shifted absorption than the 7-donor substituted coumarins (PS2, PS4, and PS6). The chemical potential (μ) and electrophilicity index (ω) showed direct relation with the band gap and an inverse relation with chemical hardness (η) and hyperhardness (Γ). The global reactivity descriptors μ and ω showed direct and η and Γ showed an inverse correlation with first-order hyperpolarizability (β0) and second-order hyperpolarizability (γ). The β0 and γ for 7-donor substituted coumarin are higher than for 6-donor substituted coumarin.
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Affiliation(s)
- Puja O Gupta
- Department of Dyestuff Technology (Currently named Department of Speciality Chemicals Technology), Institute of Chemical Technology, N. P. Marg, Matunga, Mumbai 400019, Maharashtra, India
| | - Suryapratap J Sharma
- Department of Dyestuff Technology (Currently named Department of Speciality Chemicals Technology), Institute of Chemical Technology, N. P. Marg, Matunga, Mumbai 400019, Maharashtra, India
| | - Nagaiyan Sekar
- Department of Dyestuff Technology (Currently named Department of Speciality Chemicals Technology), Institute of Chemical Technology, N. P. Marg, Matunga, Mumbai 400019, Maharashtra, India.
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Arumugam T, Ramalingam A, Guerroudj AR, Sambandam S, Boukabcha N, Chouaih A. Conformation and vibrational spectroscopic analysis of 2,6-bis(4-fluorophenyl)-3,3-dimethylpiperidin-4-one (BFDP) by DFT method: A potent anti-Parkinson's, anti-lung cancer, and anti-human infectious agent. Heliyon 2023; 9:e21315. [PMID: 37954314 PMCID: PMC10637958 DOI: 10.1016/j.heliyon.2023.e21315] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/16/2023] [Accepted: 10/19/2023] [Indexed: 11/14/2023] Open
Abstract
The potential of 2,6-bis(4-fluorophenyl)-3,3-dimethylpiperidin-4-one (BFDP) as an anti-Parkinson's, anti-lung cancer, and anti-human infectious agent was extensively assessed in the current study. To accomplish this, the compound BFDP was synthesised and analysed using several spectroscopic approaches, such as NMR, mass and FT-IR spectral studies. The computational calculations for the molecule were carried out using density functional theory (DFT) at the B3LYP/6-311G++ (d,p) level of theory. A X-ray diffraction (XRD) study allows us to analyse the crystalline structure of our BFDP molecule. Intermolecular interactions were assessed using 3D Hirshfeld surfaces (3D-HS) and 2D fingerprint plots. AIM and NCI-RDG were done using quantum calculations and the DFT technique, and topological ELF and LOL, as well as vibrational parameters, have been obtained. The thermodynamic and thermal properties of the BFDP compound were determined. To investigate the pharmacokinetic characteristics of BFDP, a molecular docking study and an in silico ADMET study were done.
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Affiliation(s)
- Thangamani Arumugam
- Department of Chemistry, Karpagam Academy of Higher Education, Coimbatore 641 021, Tamil Nadu, India
- Centre for Material Chemistry, Karpagam Academy of Higher Education, Coimbatore 641 021, Tamil Nadu, India
| | - Arulraj Ramalingam
- Department of Electrical and Computer Engineering, National University of Singapore, 117 583, Singapore
| | - Ahlam Roufieda Guerroudj
- Laboratory of Technology and Solid Properties (LTPS), Abdelhamid Ibn Badis University of Mostaganem, 27000 Mostaganem, Algeria
| | - Sivakumar Sambandam
- Research and Development Centre, Bharathiar University, Coimbatore 641 046, Tamil Nadu, India
- BPJ College of Arts and Science, Kozhai, Srimushnam, Cuddalore 608703, Tamil Nadu, India
| | - Nourdine Boukabcha
- Laboratory of Technology and Solid Properties (LTPS), Abdelhamid Ibn Badis University of Mostaganem, 27000 Mostaganem, Algeria
- Chemistry Department, Faculty of Exact Sciences and Informatic, Hassiba Benbouali University, Chlef, 02000, Algeria
| | - Abdelkader Chouaih
- Laboratory of Technology and Solid Properties (LTPS), Abdelhamid Ibn Badis University of Mostaganem, 27000 Mostaganem, Algeria
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Basha AA, Ali Khan FL, Kubaib A, Imran PM, Nebbache N. Ternary Mixture of Pentanamide in Solvent Analogy with Halogenated Phenol: Experimental, Theoretical, and In Silico Biological Studies. ACS OMEGA 2023; 8:33928-33942. [PMID: 37744853 PMCID: PMC10515181 DOI: 10.1021/acsomega.3c04710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 08/14/2023] [Indexed: 09/26/2023]
Abstract
This research describes the preparation of mixtures of new halogen-substituted phenol derivatives and their effects due to linkages with a fatty amide (pentanamide). The molecules were optimized using DFT, and the vibrational and electronic analysis was done subsequently. The energies of frontier molecular orbitals (FMOs) were used to estimate the global chemical reactivity parameters as we suggest that hydrogen-bonded networks may have contributed to the stability and reactivity of the compound. In addition to the experimental investigation, dielectric parameters were calculated. Fukui functions were analyzed to study the chemical reactivity. To get insight into interactions of σ → π* orbitals, natural bond orbital calculations were done. Additionally, surface analysis of the MEP and Hirshfeld charges were performed at the equivalent DFT levels. The research also indicated that both (interaction region indicator) IRI and (electron delocalize range) EDR would proficiently identify chemical-bonding and weak interaction regions, providing a significant advantage in exploring diverse chemical systems and reactions. This indicated that compounds could diffuse through noncovalent interactions, including intramolecular hydrogen bonding. Dielectric relaxation studies taken at five distinct molar ratios identified significant dielectric properties such as ε', ε″, ε0, and ε∞. The PA with FP, CP, BP, and IP molecules has potential antiviral and antioxidant benefits for carbonic anhydrase, with favorable drug-like features and diverse biological benefits. Pharmacological effects were forecasted using the PASS server, and these molecules exhibited favorable pharmacokinetic properties.
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Affiliation(s)
- A. Aathif Basha
- Department
of Physics, Islamiah College (Autonomous), Vaniyambadi 635752, Tamilnadu, India
| | - F. Liakath Ali Khan
- Department
of Physics, Islamiah College (Autonomous), Vaniyambadi 635752, Tamilnadu, India
| | - Attar Kubaib
- Department
of Chemistry, Islamiah College (Autonomous), Vaniyambadi 635752, Tamilnadu, India
| | | | - Nadia Nebbache
- Laboratory
of Applied Chemistry, University of Biskra, BP 145, 07000 Biskra, Algeria
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Synthesis, Empirical and Theoretical Investigations on New Histaminium Bis(Trioxonitrate) Compound. Molecules 2023; 28:molecules28041931. [PMID: 36838921 PMCID: PMC9958629 DOI: 10.3390/molecules28041931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
In this paper, a novel hybrid material, entitled histaminium bis(trioxonitrate), with the general chemical formula (C5H11N3)(NO3)2, denoted by HTN was presented. Single-crystal X-ray diffraction was used to determine the structural characteristics of this compound after it was made using a slow evaporation method at room temperature. This compound was elaborated and crystallized to the monoclinic system with space group P21/c, and the lattice parameters obtained were: a = 10.4807 (16)Å, b = 11.8747 (15)Å, c = 16.194 (2)Å, β = 95.095 (6)°, V = 2007.4 (5)Å3 and Z = 8. The title compound's atomic structure couldbe modeled as a three-dimensional network. Organic cations and nitrate anions were connected via N-H...O and C-H...O hydrogen bonds in the HTN structure. The intermolecular interactions responsible for the formation of crystal packing were evaluated using Hirshfeld surfaces and two-dimensional fingerprint plots. The compound's infrared spectrum, which ranged from 4000 to 400 cm-1, confirmed the presence of the principal bands attributed to the internal modes of the organic cation and nitrate anions. Additionally, spectrofluorimetry and the ultraviolet-visible spectrum was used to investigate this compound. DFT calculations were used to evaluate the composition and properties of HTN. The energy gap, chemical reactivity and crystal stability of HTN were quantified by performing HOMO-LUMO frontier orbitals analysis. Topological analysis (AIM), Reduced Density Gradient (RDG), molecular electrostatic potential surface (MEPS) and Mulliken population were processed to determine the types of non-covalent interactions, atomic charges and molecular polarity in detail.
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Sharma SJ, Sekar N. Charge Transfer as Bridging Correlator for DSSC Efficiency and NLO Property. ChemistrySelect 2022. [DOI: 10.1002/slct.202203262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Affiliation(s)
- Suryapratap J. Sharma
- Dyestuff Technology Department (Currently named Department of Specialty Chemicals Technology) Institute of Chemical Technology Nathalal Parekh Marg, Matunga Mumbai 400019 Maharashtra India
| | - Nagaiyan Sekar
- Dyestuff Technology Department (Currently named Department of Specialty Chemicals Technology) Institute of Chemical Technology Nathalal Parekh Marg, Matunga Mumbai 400019 Maharashtra India
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Jomaa I, Issaoui N, Roisnel T, Marouani H. Assembly of two new hybrid chloride materials with potential NLO properties: Structure elucidation, empirical and computational studies. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2022. [DOI: doi.org/10.1007/s13738-021-02469-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Jomaa I, Issaoui N, Roisnel T, Marouani H. Assembly of two new hybrid chloride materials with potential NLO properties: Structure elucidation, empirical and computational studies. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2022. [DOI: 10.1007/s13738-021-02469-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Prabukanthan P, Bhakyajothi V, Kumar MS, Harichandran G, Dinakaran K, Seenuvasakumaran P. Synthesis, spectroscopic analysis and DFT studies of N-(2-methyl-5-nitro-phenyl)benzamide organic single crystal. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.131172] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Medimagh M, Issaoui N, Gatfaoui S, Antonia Brandán S, Al-Dossary O, Marouani H, J. Wojcik M. Impact of non-covalent interactions on FT-IR spectrum and properties of 4-methylbenzylammonium nitrate. A DFT and molecular docking study. Heliyon 2021; 7:e08204. [PMID: 34754970 PMCID: PMC8556648 DOI: 10.1016/j.heliyon.2021.e08204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 07/09/2021] [Accepted: 10/14/2021] [Indexed: 01/18/2023] Open
Abstract
In this research, the impact of non-covalent interactions on the FT-IR spectrum and structural, electronic, topological and vibrational properties of hybrid 4-methylbenzylammonium nitrate (4MBN) have been studied combining B3LYP/CC-PVTZ calculations with molecular docking. 4MBN was synthesized and characterized by using the FT-IR spectrum while the optimized structures in gas phase and in ethanol and aqueous solutions have evidenced monodentate coordination between the nitrate and methylbenzylammonium groups, in agreement with that experimental determined for this species by X-ray diffraction. Here, non-covalent interactions were deeply analyzed in terms of topological parameters (AIM), electron localization function (ELF), localized orbital locator (LOL), Hirshfeld surface and reduced density gradient (RDG) method. Weak interactions such as H-bonds, VDW and steric effect in 4MBN were visualized and quantified by the independent gradient density (IGM) based on the promolecular density. The hyper-conjugative and the delocalization of charge in 4MBN have been elucidated by natural bonding orbital (NBO) while its chemical reactivity was studied and discussed by using molecular electrostatic potential surface (MESP), frontier molecular orbital (FMOs), density of state (DOS) and partial density of state (PDOS). The complete vibrational assignments of 69 vibration modes expected for 4MBN are reported together with the scaled force constants while the electronic transitions were evaluated by TD-DFT calculations in ethanol solution. Thermal analysis (DTA and DSC) was also determined. Molecular docking calculations have suggested that 4MBN presents biological activity and could act as a good inhibitor against schizophrenia disease.
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Affiliation(s)
- Mouna Medimagh
- University of Monastir, Laboratory of Quantum and Statistical Physics (LR18ES18), Faculty of Sciences, Monastir, 5079, Tunisia
| | - Noureddine Issaoui
- University of Monastir, Laboratory of Quantum and Statistical Physics (LR18ES18), Faculty of Sciences, Monastir, 5079, Tunisia
| | - Sofian Gatfaoui
- University of Carthage, Laboratory of Chemistry of Materials (LR13ES08), Faculty of Sciences of Bizerte, 7021, Tunisia
| | - Silvia Antonia Brandán
- Cátedra de Química General, Instituto de Química Inorgánica, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Ayacucho 471, 4000, San Miguel de Tucumán, Tucumán, Argentina
| | - Omar Al-Dossary
- Department of Physics and Astronomy, College of Science, King Saud University, PO Box 2455, Riyadh, 11451, Saudi Arabia
| | - Houda Marouani
- University of Carthage, Laboratory of Chemistry of Materials (LR13ES08), Faculty of Sciences of Bizerte, 7021, Tunisia
| | - Marek J. Wojcik
- Faculty of Chemistry, Jagiellonian University, 30-387 Krakow, Gronostajowa 2, Poland
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