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Regio- and stereochemical aspects in the functionalisation of a lithiated 2-(3-chloro-2-methyl-1-propenyl)-2-oxazoline: electrophile and temperature effects. Tetrahedron 2015. [DOI: 10.1016/j.tet.2015.06.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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2
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Zheng S, Pfaendtner J. Enhanced sampling of chemical and biochemical reactions with metadynamics. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2014.923574] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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De Meyer T, Hemelsoet K, Van der Schueren L, Pauwels E, De Clerck K, Van Speybroeck V. Investigating the halochromic properties of azo dyes in an aqueous environment by using a combined experimental and theoretical approach. Chemistry 2012; 18:8120-9. [PMID: 22614919 DOI: 10.1002/chem.201103633] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Revised: 01/25/2012] [Indexed: 11/05/2022]
Abstract
The halochromism in solution of a prototypical example of an azo dye, ethyl orange, was investigated by using a combined theoretical and experimental approach. Experimental UV/Vis and Raman spectroscopy pointed towards a structural change of the azo dye with changing pH value (in the range pH 5-3). The pH-sensitive behavior was modeled through a series of ab initio computations on the neutral and various singly and doubly protonated structures. For this purpose, contemporary DFT functionals (B3LYP, CAM-B3LYP, and M06) were used in combination with implicit modeling of the water solvent environment. Static calculations were successful in assigning the most-probable protonation site. However, to fully understand the origin of the main absorption peaks, a molecular dynamics simulation study in a water molecular environment was used in combination with time-dependent DFT (TD-DFT) calculations to deduce average UV/Vis spectra that take into account the flexibility of the dye and the explicit interactions with the surrounding water molecules. This procedure allowed us to achieve a remarkable agreement between the theoretical and experimental UV/Vis spectrum and enabled us to fully unravel the pH-sensitive behavior of ethyl orange in aqueous environment.
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Affiliation(s)
- Thierry De Meyer
- Center for Molecular Modeling, Ghent University, Technologiepark 903, 9052 Zwijnaarde, QCMM-Alliance Ghent-Brussels, Belgium
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Mangelinckx S, De Sterck B, Colpaert F, Catak S, Jacobs J, Rooryck S, Waroquier M, Van Speybroeck V, De Kimpe N. Diastereoselective Aldol Reaction of Zincated 3-Chloro-3-methyl-1-azaallylic Anions as Key Step in the Synthesis of 1,2,3,4-Tetrasubstituted 3-Chloroazetidines. J Org Chem 2012; 77:3415-25. [DOI: 10.1021/jo300203t] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sven Mangelinckx
- Department of Sustainable Organic
Chemistry and Technology, Faculty of Bioscience Engineering, Ghent
University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Bart De Sterck
- Center for Molecular Modeling,
Ghent University, Technologiepark 903, B-9052 Zwijnaarde, Belgium,
Member of QCMM Alliance Ghent-Brussels
| | - Filip Colpaert
- Department of Sustainable Organic
Chemistry and Technology, Faculty of Bioscience Engineering, Ghent
University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Saron Catak
- Center for Molecular Modeling,
Ghent University, Technologiepark 903, B-9052 Zwijnaarde, Belgium,
Member of QCMM Alliance Ghent-Brussels
| | - Jan Jacobs
- Department of Sustainable Organic
Chemistry and Technology, Faculty of Bioscience Engineering, Ghent
University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Stijn Rooryck
- Department of Sustainable Organic
Chemistry and Technology, Faculty of Bioscience Engineering, Ghent
University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Michel Waroquier
- Center for Molecular Modeling,
Ghent University, Technologiepark 903, B-9052 Zwijnaarde, Belgium,
Member of QCMM Alliance Ghent-Brussels
| | - Veronique Van Speybroeck
- Center for Molecular Modeling,
Ghent University, Technologiepark 903, B-9052 Zwijnaarde, Belgium,
Member of QCMM Alliance Ghent-Brussels
| | - Norbert De Kimpe
- Department of Sustainable Organic
Chemistry and Technology, Faculty of Bioscience Engineering, Ghent
University, Coupure Links 653, B-9000 Ghent, Belgium
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Popescu AR, Musteti AD, Ferrer-Ugalde A, Viñas C, Núñez R, Teixidor F. Influential Role of Ethereal Solvent on Organolithium Compounds: The Case of Carboranyllithium. Chemistry 2012; 18:3174-84. [DOI: 10.1002/chem.201102626] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Indexed: 01/27/2023]
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Verstraelen T, Bultinck P, Van Speybroeck V, Ayers PW, Van Neck D, Waroquier M. The Significance of Parameters in Charge Equilibration Models. J Chem Theory Comput 2011; 7:1750-64. [DOI: 10.1021/ct200006e] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- T. Verstraelen
- Center for Molecular Modeling, QCMM Alliance Ghent-Brussels, Ghent University, Technologiepark 903, B-9052 Zwijnaarde, Belgium
| | - P. Bultinck
- Department of Inorganic and Physical Chemistry, QCMM Alliance Ghent-Brussels, Ghent University, Krijgslaan 281 (S-3), B-9000 Gent, Belgium
| | - V. Van Speybroeck
- Center for Molecular Modeling, QCMM Alliance Ghent-Brussels, Ghent University, Technologiepark 903, B-9052 Zwijnaarde, Belgium
| | - P. W. Ayers
- Department of Chemistry, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada
| | - D. Van Neck
- Center for Molecular Modeling, QCMM Alliance Ghent-Brussels, Ghent University, Technologiepark 903, B-9052 Zwijnaarde, Belgium
| | - M. Waroquier
- Center for Molecular Modeling, QCMM Alliance Ghent-Brussels, Ghent University, Technologiepark 903, B-9052 Zwijnaarde, Belgium
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Barducci A, Bonomi M, Parrinello M. Metadynamics. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.31] [Citation(s) in RCA: 712] [Impact Index Per Article: 50.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Alessandro Barducci
- Computational Science, Department of Chemistry and Applied Biosciences, ETH Zurich, USI Campus, Lugano, Switzerland
| | - Massimiliano Bonomi
- Computational Science, Department of Chemistry and Applied Biosciences, ETH Zurich, USI Campus, Lugano, Switzerland
| | - Michele Parrinello
- Computational Science, Department of Chemistry and Applied Biosciences, ETH Zurich, USI Campus, Lugano, Switzerland
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Deora N, Carlier PR. Computational Studies of Ion-Pair Separation of Benzylic Organolithium Compounds in THF: Importance of Explicit and Implicit Solvation. J Org Chem 2010; 75:1061-9. [DOI: 10.1021/jo9016452] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Nipa Deora
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24060
| | - Paul R. Carlier
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24060
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De Sterck B, Van Speybroeck V, Mangelinckx S, Verniest G, De Kimpe N, Waroquier M. Theoretical Study on the Structural Properties of Various Solvated Metalated 3-Halo-1-azaallylic Anions. J Phys Chem A 2009; 113:6375-80. [DOI: 10.1021/jp811317y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bart De Sterck
- Center for Molecular Modeling, Ghent University, Proeftuinstraat 86, B-9000 Ghent, Belgium, and Department of Organic Chemistry, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, B-9000 Ghent, Belgium
| | - Veronique Van Speybroeck
- Center for Molecular Modeling, Ghent University, Proeftuinstraat 86, B-9000 Ghent, Belgium, and Department of Organic Chemistry, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, B-9000 Ghent, Belgium
| | - Sven Mangelinckx
- Center for Molecular Modeling, Ghent University, Proeftuinstraat 86, B-9000 Ghent, Belgium, and Department of Organic Chemistry, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, B-9000 Ghent, Belgium
| | - Guido Verniest
- Center for Molecular Modeling, Ghent University, Proeftuinstraat 86, B-9000 Ghent, Belgium, and Department of Organic Chemistry, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, B-9000 Ghent, Belgium
| | - Norbert De Kimpe
- Center for Molecular Modeling, Ghent University, Proeftuinstraat 86, B-9000 Ghent, Belgium, and Department of Organic Chemistry, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, B-9000 Ghent, Belgium
| | - Michel Waroquier
- Center for Molecular Modeling, Ghent University, Proeftuinstraat 86, B-9000 Ghent, Belgium, and Department of Organic Chemistry, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, B-9000 Ghent, Belgium
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