scholarly journals Rigorous Calculation of Free Energy Difference Between Open and Closed States of Adenylate Kinase from Explicit Solvent Molecular Dynamics

2011 ◽  
Vol 100 (3) ◽  
pp. 378a
Author(s):  
Pavel I. Zhuravlev ◽  
Davit A. Potoyan ◽  
Michael Rubinstein ◽  
Garegin A. Papoian
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Adenylate Kinase ◽  
Energy Difference ◽  
Free Energy Difference ◽  
Rigorous Calculation ◽  
Explicit Solvent

scholarly journals Solvation Free Energy of Protonated Lysine: Molecular Dynamics Study

2021 ◽  
Vol 7 (2) ◽  
pp. 69-75
Author(s):  
S. P. Khanal ◽  
B. Poudel ◽  
R. P. Koirala ◽  
N. P. Adhikari
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Energy Difference ◽  
Solvation Free Energy ◽  
Free Energy Perturbation ◽  
Free Energy Difference ◽  
Free Energy Of Solvation ◽  
Acceptance Ratio ◽  
Energy Perturbation ◽  
Dynamics Simulations

In the present work, we have used an alchemical approach for calculating solvation free energy of protonated lysine in water from molecular dynamics simulations. These approaches use a non-physical pathway between two end states in order to compute free energy difference from the set of simulations. The solute is modeled using bonded and non-bonded interactions described by OPLS-AA potential, while four different water models: TIP3P, SPC, SPC/E and TIP4P are used. The free energy of solvation of protonated lysine in water has been estimated using thermodynamic integration, free energy perturbation, and Bennett acceptance ratio methods at 310 K temperature. The contributions to the free energy due to van der Waals and electrostatics parameters are also separately computed. The estimated values of free energy of solvation using different methods are in well agreement with previously reported experimental value within 14 %.

Conformational analysis of 1,4-disubstituted cyclohexanes. III. trans-1,4-Di(trifluoroacetoxy)cyclohexane

1969 ◽  
Vol 47 (3) ◽  
pp. 429-431 ◽  
Author(s):  
Gordon Wood ◽  
E. P. Woo ◽  
M. H. Miskow
Keyword(s):  
Nuclear Magnetic Resonance ◽  
Free Energy ◽  
Magnetic Resonance ◽  
Low Temperature ◽  
Conformational Analysis ◽  
Integration Method ◽  
Standard Free Energy ◽  
Energy Difference ◽  
Free Energy Difference ◽  
Conformational Free Energy

By the low temperature nuclear magnetic resonance integration method the standard free energy difference between the diequatorial and the diaxial forms of 1-H,4-H-trans-1,4-di(trifluoroacetoxy)-cyclohexane-d8 was found to be 77 ± 5 cal/mole. The conformational free energy (−ΔG0) of the trifluoroacetoxy group in the monosubstituted cyclohexane was 485 ± 4 cal/mole at the same temperature. The non-additivity of the −ΔG0 values is discussed in terms of transannular electrostatic interaction.

A comprehensive computational examination of transannular Diels–Alder reactions of unsubstituted C14 trienes — Barriers, template effects, and the Curtin–Hammett principle

2001 ◽  
Vol 79 (8) ◽  
pp. 1284-1292 ◽  
Author(s):  
Saul Wolfe ◽  
Anthony V Buckley ◽  
Noham Weinberg
Keyword(s):  
Free Energy ◽  
Energy Difference ◽  
Diels Alder ◽  
Molecular Orbital Calculations ◽  
Free Energy Difference ◽  
Molecular Mechanics Calculations ◽  
Geometrical Isomers ◽  
Free Energy Of Activation ◽  
Transition Structures ◽  
Cyclic Compounds

A combination of MM3-level molecular mechanics calculations and PM3-level semiempirical molecular orbital calculations has been employed, in conjunction with an algorithm for the comprehensive conformational analysis of cyclic compounds, to obtain 1202 unique 1,3,9-cyclotetradecatriene conformations, distributed over the six possible geometrical isomers, and 70 unique transannular Diels–Alder transition structures leading to the six possible stereoisomeric tricyclic olefins. A kinetic analysis that takes into account all minima of a given geometrical isomer and all transition structures leading to the same tricyclic product leads to a free energy of activation that is almost the same as the free energy difference between the lowest minimum and the lowest transition structure (the Curtin–Hammett principle). A substantial template effect, mainly entropic in origin, is found when the transannular reactions are compared to the Diels–Alder reactions of the cognate 2,4-hexatrienes with the 2-butenes. Although the cyclization of the trans-cis-trans triene favours the cis-anti-cis over the trans-anti-trans product by more than 20 kcal mol–1, the situation is reversed in the acyclic reaction. A cyclic triene that can cyclize directly to a trans-anti-trans tricycle can therefore be proposed.Key words: molecular models, Deslongchamps, Takahashi, trans-anti-trans tricycle, MM3, PM3, transition states.

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