Topography of the Free Energy Landscape on the Claisen-Schmidt Condensation: Solvent and Temperature Effect in the Rate-Controlling Step

2021 ◽  
Author(s):  
Nayara Dantas Coutinho ◽  
Hugo Gontijo Machado ◽  
Valter Henrique Carvalho-Silva ◽  
Wender A. Silva
Keyword(s):  
Free Energy ◽  
Temperature Effect ◽  
Strong Influence ◽  
Aldol Condensation ◽  
Energy Landscape ◽  
Bond Formation ◽  
Free Energy Landscape ◽  
Rate Controlling Step ◽  
Formation Step

Recent studies have assigned hydroxide elimination and C=C bond formation step in base-promoted aldol condensation the role of having a strong influence in the overall rate reaction, in contrast to...

Reply to the ‘Comment on “Topography of the Free Energy Landscape on the Claisen–Schmidt Condensation: Solvent and Temperature Effect in the Rate-Controlling Step”’ by N. D. Coutinho, H. G. Machado, V. H. Carvalho-Silva and W. A. da Silva, Phys. Chem. Chem. Phys., 2021, 23, 6738

2021 ◽  
Vol 23 (38) ◽  
pp. 22202-22206
Author(s):  
Nayara Dantas Coutinho ◽  
Hugo Gontijo Machado ◽  
Valter Henrique Carvalho-Silva ◽  
Wender Alves da Silva
Keyword(s):  
Free Energy ◽  
Temperature Effect ◽  
Energy Landscape ◽  
Chem Phys ◽  
Free Energy Landscape ◽  
Hybrid Treatment ◽  
Limiting Step ◽  
Rate Controlling Step ◽  
Phys Chem Chem Phys

New calculations improved by explicit-implicit hybrid treatment ensure that the overall iKIE > 1 does not exclude step R4 as a limiting-step and that the debate about the infallibility of the generalization of step R5 as RCS is reasonable.

scholarly journals On the Role of Enthalpic and Entropic Contributions on the Conformational Free Energy Landscape of MIL-101(Cr) Structural Building Units

2019 ◽  
Author(s):  
Loukas Kollias ◽  
David Cantu ◽  
Vassiliki-Alexandra Glezakou ◽  
Roger Rousseau ◽  
Matteo Salvalaglio
Keyword(s):  
Free Energy ◽  
Metal Organic Framework ◽  
Energy Landscape ◽  
Ionic Species ◽  
Free Energy Landscape ◽  
Materials Synthesis ◽  
Factors Affecting ◽  
Enthalpy And Entropy ◽  
Conformational Free Energy

The thermostructural behavior of metal-organic framework (MOF) precursors is responsible for regulating the introduction of MOF structure defects during synthesis. In this paper, we evaluate factors affecting the flexibility of MIL-101(Cr) half – secondary building units (half-SBUs) in solution using enhanced sampling methods. In particular, we calculate entropic and enthalpic contributions to the conformational free energy landscape of isolated MIL-101(Cr) half-SBUs, in water, in the presence and absence of ionic species (Na<sup>+</sup> and F<sup>-</sup>), and in N, N-dimethylformamide (DMF). We find that the interplay between enthalpy and entropy determines the most probable conformational state for half-SBUs. Furthermore, we investigate the role of enthalpy and entropy in the conformational rearrangement of an SBU in water, noting that entropic contributions are essential to stabilize configurations that depart from those coherent with the MIL-101(Cr) crystal structure. Our analysis highlights the importance of explicitly considering entropic effects on the configurational ensembles of MOF building units, as such effects can significantly impact the relative stability of structurally different conformers, which ultimately can be responsible for the formation of defects during materials synthesis.

scholarly journals On the Role of Enthalpic and Entropic Contributions on the Conformational Free Energy Landscape of MIL-101(Cr) Structural Building Units

2019 ◽  
Author(s):  
Loukas Kollias ◽  
David Cantu ◽  
Vassiliki-Alexandra Glezakou ◽  
Roger Rousseau ◽  
Matteo Salvalaglio
Keyword(s):  
Free Energy ◽  
Metal Organic Framework ◽  
Energy Landscape ◽  
Ionic Species ◽  
Free Energy Landscape ◽  
Materials Synthesis ◽  
Factors Affecting ◽  
Enthalpy And Entropy ◽  
Conformational Free Energy

The thermostructural behavior of metal-organic framework (MOF) precursors is responsible for regulating the introduction of MOF structure defects during synthesis. In this paper, we evaluate factors affecting the flexibility of MIL-101(Cr) half – secondary building units (half-SBUs) in solution using enhanced sampling methods. In particular, we calculate entropic and enthalpic contributions to the conformational free energy landscape of isolated MIL-101(Cr) half-SBUs, in water, in the presence and absence of ionic species (Na<sup>+</sup> and F<sup>-</sup>), and in N, N-dimethylformamide (DMF). We find that the interplay between enthalpy and entropy determines the most probable conformational state for half-SBUs. Furthermore, we investigate the role of enthalpy and entropy in the conformational rearrangement of an SBU in water, noting that entropic contributions are essential to stabilize configurations that depart from those coherent with the MIL-101(Cr) crystal structure. Our analysis highlights the importance of explicitly considering entropic effects on the configurational ensembles of MOF building units, as such effects can significantly impact the relative stability of structurally different conformers, which ultimately can be responsible for the formation of defects during materials synthesis.

scholarly journals Role of Small Oligomers on the Amyloidogenic Aggregation Free-Energy Landscape

2010 ◽  
Vol 395 (1) ◽  
pp. 134-154 ◽  
Author(s):  
Xianglan He ◽  
Jason T. Giurleo ◽  
David S. Talaga
Keyword(s):  
Free Energy ◽  
Energy Landscape ◽  
Free Energy Landscape

scholarly journals On the Role of Enthalpic and Entropic Contributions to the Conformational Free Energy Landscape of MIL‐101(Cr) Secondary Building Units

2020 ◽  
Vol 3 (12) ◽  
pp. 2000092
Author(s):  
Loukas Kollias ◽  
David C. Cantu ◽  
Vassiliki‐Alexandra Glezakou ◽  
Roger Rousseau ◽  
Matteo Salvalaglio
Keyword(s):  
Free Energy ◽  
Energy Landscape ◽  
Free Energy Landscape ◽  
Secondary Building Units ◽  
Conformational Free Energy

scholarly journals On the Role of Enthalpic and Entropic Contributions on the Conformational Free Energy Landscape of MIL-101(Cr) Structural Building Units

2020 ◽  
Author(s):  
Loukas Kollias ◽  
David Cantu ◽  
Vassiliki-Alexandra Glezakou ◽  
Roger Rousseau ◽  
Matteo Salvalaglio
Keyword(s):  
Free Energy ◽  
Metal Organic Framework ◽  
Energy Landscape ◽  
Ionic Species ◽  
Free Energy Landscape ◽  
Factors Affecting ◽  
Secondary Building Units ◽  
Enthalpy And Entropy ◽  
Conformational Free Energy

The thermo-structural behavior of metal-organic framework (MOF) precursors is responsible for regulating the introduction of defects in MOF structures during synthesis. In this paper, factors affecting the flexibility of MIL-101(Cr) half-secondary building units (half-SBUs) are evaluated in solution using enhanced sampling methods. In particular, entropic and enthalpic contributions to the conformational free energy landscape of isolated MIL-101(Cr) half-SBUs are calculated in water, in the presence and absence of ionic species (Na<sup>+</sup> and F<sup>-</sup>), and in N, N-dimethylformamide (DMF). This analysis leads to the observation that the interplay between enthalpy and entropy determines the most probable conformational state for half-SBUs. Furthermore, the role of enthalpy and entropy in the conformational rearrangement of an SBU is investigated in water, noting that entropic contributions are essential to stabilize configurations that depart from those coherent with the MIL-101(Cr) crystal structure. This analysis highlights the importance of explicitly considering entropic effects on the configurational ensembles of MOF building units and highlights the significant impact they have on the relative stability of crystal-like and non-crystal-like conformers.

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