scholarly journals Polymer Glass Formation: Role of Activation Free Energy, Configurational Entropy, and Collective Motion

2021 ◽  
Vol 54 (7) ◽  
pp. 3001-3033 ◽  
Author(s):  
Wen-Sheng Xu ◽  
Jack F. Douglas ◽  
Zhao-Yan Sun
Keyword(s):  
Free Energy ◽  
Glass Formation ◽  
Collective Motion ◽  
Configurational Entropy ◽  
Activation Free Energy ◽  
Polymer Glass

Elucidating the role of solvents in acid catalyzed dehydration of biorenewable hydroxy-lactones

2020 ◽  
Vol 5 (4) ◽  
pp. 651-662 ◽  
Author(s):  
Gourav Shrivastav ◽  
Tuhin S. Khan ◽  
Manish Agarwal ◽  
M. Ali Haider
Keyword(s):  
Free Energy ◽  
Transition State ◽  
Energy Barrier ◽  
Free Energy Barrier ◽  
Activation Free Energy ◽  
Acid Catalyzed

Utilizing the differential stabilization of reactant and transition state in the polar and apolar solvents to lower the activation free energy barrier for acid-catalyzed dehydration of hydroxy lactones.

Exploring the role of ions and amino acids in directing the growth of minerals from solution

2008 ◽  
Vol 72 (1) ◽  
pp. 273-276 ◽  
Author(s):  
S. Piana ◽  
F. Jones ◽  
Z. Taylor ◽  
P. Raiteri ◽  
J. D. Gale
Keyword(s):  
Amino Acids ◽  
Computer Simulation ◽  
Free Energy ◽  
Aspartic Acid ◽  
Morphology Control ◽  
New Approach ◽  
Activation Free Energy

AbstractThe influence of both sulphate ions and aspartic acid on directing the growth of baryte has been explored using computer simulation. Both species are found to significantly reduce the activation free-energy to growth under appropriate conditions, with the influence of sulphate being surface specific. This offers the potential for a new approach to morphology control without inhibition that may have implications for biomineralization.

scholarly journals Quantitative relations between cooperative motion, emergent elasticity, and free volume in model glass-forming polymer materials

2015 ◽  
Vol 112 (10) ◽  
pp. 2966-2971 ◽  
Author(s):  
Beatriz A. Pazmiño Betancourt ◽  
Paul Z. Hanakata ◽  
Francis W. Starr ◽  
Jack F. Douglas
Keyword(s):  
Free Volume ◽  
Glass Formation ◽  
Collective Motion ◽  
Configurational Entropy ◽  
Polymer Melt ◽  
Polymer Materials ◽  
Coarse Grained ◽  
Glass Forming ◽  
Cooperative Motion ◽  
Glass Forming Materials

The study of glass formation is largely framed by semiempirical models that emphasize the importance of progressively growing cooperative motion accompanying the drop in fluid configurational entropy, emergent elasticity, or the vanishing of accessible free volume available for molecular motion in cooled liquids. We investigate the extent to which these descriptions are related through computations on a model coarse-grained polymer melt, with and without nanoparticle additives, and for supported polymer films with smooth or rough surfaces, allowing for substantial variation of the glass transition temperature and the fragility of glass formation. We find quantitative relations between emergent elasticity, the average local volume accessible for particle motion, and the growth of collective motion in cooled liquids. Surprisingly, we find that each of these models of glass formation can equally well describe the relaxation data for all of the systems that we simulate. In this way, we uncover some unity in our understanding of glass-forming materials from perspectives formerly considered as distinct.

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.

scholarly journals Theoretical insights into C–H bond activation of methane by transition metal clusters: the role of anharmonic effects

2021 ◽  
Author(s):  
Preeti Bhumla ◽  
Manish Kumar ◽  
Saswata Bhattacharya
Keyword(s):  
Free Energy ◽  
Md Simulation ◽  
Bond Activation ◽  
Integration Method ◽  
Excess Free Energy ◽  
Configurational Entropy ◽  
Transition Metal Clusters ◽  
Vibrational Free Energy ◽  
Free Energy Contribution

To incorporate the anharmonicity in the vibrational free energy contribution to the configurational entropy, we evaluate the excess free energy of clusters numerically by a thermodynamic integration method with ab initio molecular dynamics (aiMD) simulation inputs.

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...

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