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Zouaoui-Rabah M, Bekri L, Hedidi M, Elhorri AM, Madaoui Y. Characteristics of new pyrrolic derivatives and their oligomers using DFT and TD-DFT calculations. J Mol Model 2023; 29:364. [PMID: 37945908 DOI: 10.1007/s00894-023-05763-6] [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: 08/31/2023] [Accepted: 10/22/2023] [Indexed: 11/12/2023]
Abstract
CONTEXT This article is based on the study of pyrrolic derivatives and their oligomers. Knowing that, pyrrolic derivatives are widely studied on an industrial scale. The aim of this work is to find pyrrolic derivatives having the same physicochemical characteristics such as the pyrrolic edifice. Six derivatives were studied by substituting the hydrogens in the β position of the pyrroles with the following radicals: -CHO, -Cl, -CN, -NO, and -OH. The study was carried out theoretically using ab initio and density functional of theory (DFT) methods. In the first step, molecules of four units were taken into consideration in order to make the comparison between them. This comparison showed that the majority of molecules exhibited high intramolecular charge transfer (ICT) compared to the molecule composed of four pyrrolic units (OP4), and also exhibited strong nucleophilic and electrophilic characteristics. Natural bond orbital (NBO) analysis has shown continuous ICT mechanisms for certain molecules. The studied derivatives showed good solvation in several solvents compared to OP4. The molecules substituted by the radicals -CHO, -CN, -OH, and -NO generated several peaks in the excited states, which is the opposite case for the other molecules with a single peak. The effects of chain elongation revealed exponential equations generated by the two parameters energy gaps (ΔEH-L) and maximum wavelengths (λmax) as a function of the number of units (n). These equations were used to predict the maximum and minimum values of the above parameters for more elongated oligomers. METHOD The software used to make the calculations is Gaussian 16. All geometries were calculated by B3LYP functional and 6-31++G(d,p) basis set. The electronic parameters ΔEH-L were calculated by the following functionals: B3LYP, CAM-B3LYP, LC-wPBE, LC-BLYP, wB97X, M062X, M06HF, and M11 in addition to the second-order Møller-Plesset method (MP2) while always keeping the basis set mentioned before. An effect of basis set variation was studied by the optimal functional in combination with the following basis sets: 6-31G(d,p), 6-31++G(d,p), cc-pVDZ, AUG-cc-pVDZ, 6-311G(d,p), 6-311++G(d,p), cc-pVTZ, and AUG-cc-pVTZ. The NBO study was carried out with the M06HF/6-31++G(d,p) functional using the NBO method. The solvation parameters were calculated by M06HF/6-31++G(d,p) in the presence of the implicit solvation model Solvation Model based on Density (SMD). The excited states were calculated by M06HF/6-31++G(d,p) by the implicit solvation model Conductor Polarizable Continuum Model (CPCM).
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Affiliation(s)
- Mourad Zouaoui-Rabah
- Department of Preparatory Education in Science and Technology, National Polytechnic School of Oran Maurice Audin, P.O. Box 1523, Oran, El M'naouer, Algeria
- Laboratory of Materials Chemistry Catalysis and Reactivity, Department of Chemistry, Faculty of Exact Sciences and Informatics, Hassiba Benbouali University of Chlef, P.O. Box 78C, 02180, Ouled Fares Chlef, Algeria
| | - Lahcène Bekri
- Departement of Chemistry, Faculty of Exact Sciences, Mustapha Stambouli, University of Mascara, Av. Cheikh El Khaldi, 29000, Mascara, Algeria
| | - Madani Hedidi
- Laboratory of Materials Chemistry Catalysis and Reactivity, Department of Chemistry, Faculty of Exact Sciences and Informatics, Hassiba Benbouali University of Chlef, P.O. Box 78C, 02180, Ouled Fares Chlef, Algeria
- Departement of Chemistry, Faculty of Exact Sciences and Informatics, Hassiba Benbouali University of Chlef, P.O. Box 78C, 02180, Ouled Fares Chlef, Algeria
| | - Abdelkader M Elhorri
- Laboratory of Materials Chemistry Catalysis and Reactivity, Department of Chemistry, Faculty of Exact Sciences and Informatics, Hassiba Benbouali University of Chlef, P.O. Box 78C, 02180, Ouled Fares Chlef, Algeria.
- Departement of Chemistry, Faculty of Exact Sciences and Informatics, Hassiba Benbouali University of Chlef, P.O. Box 78C, 02180, Ouled Fares Chlef, Algeria.
| | - Yemouna Madaoui
- Departement of Chemistry, Faculty of Exact Sciences and Informatics, Hassiba Benbouali University of Chlef, P.O. Box 78C, 02180, Ouled Fares Chlef, Algeria
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Borges R, Colby SM, Das S, Edison AS, Fiehn O, Kind T, Lee J, Merrill AT, Merz KM, Metz TO, Nunez JR, Tantillo DJ, Wang LP, Wang S, Renslow RS. Quantum Chemistry Calculations for Metabolomics. Chem Rev 2021; 121:5633-5670. [PMID: 33979149 PMCID: PMC8161423 DOI: 10.1021/acs.chemrev.0c00901] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Indexed: 02/07/2023]
Abstract
A primary goal of metabolomics studies is to fully characterize the small-molecule composition of complex biological and environmental samples. However, despite advances in analytical technologies over the past two decades, the majority of small molecules in complex samples are not readily identifiable due to the immense structural and chemical diversity present within the metabolome. Current gold-standard identification methods rely on reference libraries built using authentic chemical materials ("standards"), which are not available for most molecules. Computational quantum chemistry methods, which can be used to calculate chemical properties that are then measured by analytical platforms, offer an alternative route for building reference libraries, i.e., in silico libraries for "standards-free" identification. In this review, we cover the major roadblocks currently facing metabolomics and discuss applications where quantum chemistry calculations offer a solution. Several successful examples for nuclear magnetic resonance spectroscopy, ion mobility spectrometry, infrared spectroscopy, and mass spectrometry methods are reviewed. Finally, we consider current best practices, sources of error, and provide an outlook for quantum chemistry calculations in metabolomics studies. We expect this review will inspire researchers in the field of small-molecule identification to accelerate adoption of in silico methods for generation of reference libraries and to add quantum chemistry calculations as another tool at their disposal to characterize complex samples.
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Affiliation(s)
- Ricardo
M. Borges
- Walter
Mors Institute of Research on Natural Products, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | - Sean M. Colby
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Susanta Das
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Arthur S. Edison
- Departments
of Genetics and Biochemistry and Molecular Biology, Complex Carbohydrate
Research Center and Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602, United States
| | - Oliver Fiehn
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
| | - Tobias Kind
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
| | - Jesi Lee
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Amy T. Merrill
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Kenneth M. Merz
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Thomas O. Metz
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Jamie R. Nunez
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Dean J. Tantillo
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Lee-Ping Wang
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Shunyang Wang
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Ryan S. Renslow
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
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Theoretical study by DFT of organometallic complexes based on metallocenes active in NLO. J Mol Model 2021; 27:179. [PMID: 34023937 DOI: 10.1007/s00894-021-04797-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 05/11/2021] [Indexed: 10/21/2022]
Abstract
This study is based on the valuation of a few model molecules. The objective of this research is focused on linear optical (LO) and nonlinear optical (NLO) enhancement of five organometallic molecules based on different metallocenes. These molecules were subjected to several calculations by different long-range functionals CAM-B3LYP, LC-BLYP, LC-wPBE, wB97X, M11, and the following three Minnesota functionals: M06-2X and M08-HX in comparison with the MP2 approach. Hence, the CAM-B3LYP functional gave the closest NLO values to the MP2 method. Second, molecule 3A based on nickelocene recorded the highest static (βtot) value which is 76.46 Χ 10-30 esu and 4803.4 Χ 10-30 esu under the laser wavelength λ = 532 nm. Third, intramolecular charge transfers (ICTs) of the molecules studied are all directed in both directions (donor to acceptor and vice versa). Finally, the specific solvent for molecules 2A and 3A is acetonitrile, and the maximum wavelengths obtained for the isolated or solvated molecule are all located in the near UV; the corresponding interval is between 250 and 395 nm. Graphical abstract.
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