scholarly journals Autonomous oscillation in supramolecular assemblies: Role of free energy landscape and fluctuations

2015 ◽  
Vol 437 ◽  
pp. 442-456
Author(s):  
Yuriy V. Sereda ◽  
Peter J. Ortoleva
Keyword(s):  
Free Energy ◽  
Energy Landscape ◽  
Supramolecular Assemblies ◽  
Free Energy Landscape

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...

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.

scholarly journals Exploring the Free Energy Landscape and Thermodynamics of Protein-Protein Association: HIV-1 Integrase Multimerization Induced by an Allosteric Inhibitor

2020 ◽  
Author(s):  
C. Tse ◽  
L. Wickstrom ◽  
M. Kvaratskhelia ◽  
E. Gallicchio ◽  
R. Levy ◽  
...  
Keyword(s):  
Free Energy ◽  
Energy Landscape ◽  
Critical Role ◽  
Configurational Entropy ◽  
Umbrella Sampling ◽  
Free Energy Landscape ◽  
Drug Induced ◽  
Protein Association ◽  
Hiv 1

AbstractWe report the free energy landscape and thermodynamics of the protein-protein association responsible for the drug-induced multimerization of HIV-1 integrase (IN). Allosteric HIV-1 integrase inhibitors (ALLINIs) promote aberrant IN multimerization by bridging IN-IN intermolecular interactions. However, the thermodynamic driving forces and kinetics of the multimerization remain largely unknown. Here we explore the early steps in the IN multimerization by using umbrella sampling and unbiased molecular dynamics simulations in explicit solvent. In direct simulations, the two initially separated dimers spontaneously associate to form near-native complexes that resemble the crystal structure of the aberrant tetramer. Most strikingly, the effective interaction of the protein-protein association is very short-ranged: the two dimers associate rapidly within tens of nanoseconds when their binding surfaces are separated by d ≤ 4.3 Å (less than two water diameters). Beyond this distance, the oligomerization kinetics appears to be diffusion controlled with a much longer association time. The free energy profile also captured the crucial role of ALLINI in promoting multimerization, and explained why several CTD mutations are remarkably resistant to the drug-induced multimerization. The results also show that at small separation the protein-protein binding process contains two consecutive phases with distinct thermodynamic signatures. First, inter-protein water molecules are expelled to the bulk resulting in a small increase in entropy, as the solvent entropy gain from the water release is nearly cancelled by the loss of side chain entropies as the two proteins approach each other. At shorter distances, the two dry binding surfaces adapt to each other to optimize their interaction energy at the expense of further protein configurational entropy loss. While the binding interfaces feature clusters of hydrophobic residues, overall, the protein-protein association in this system is driven by enthalpy and opposed by entropy.Statement of SignificanceElucidating the energetics and thermodynamic aspects of protein-protein association is important for understanding this fundamental biophysical process. This study provided a more complete physical picture of the protein-protein association responsible for the drug-induced HIV-1 integrase multimerization. The results captured the critical role of the inhibitor, and accounted for the effects of mutations on the protein association. Remarkably, the effective range of the protein-protein attractive funnel is found to be very short, at less than two layers of water, despite the fact that the two binding partners carry opposite net charges. Lastly, entropy/enthalpy decomposition shows that the solvent release from the inter-protein region into the bulk is more than offset by the loss of the solute configurational entropy due to complexation.

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