Solvent effect on the anomeric equilibrium in D-glucose: a free energy simulation analysis

1991 ◽  
Vol 113 (5) ◽  
pp. 1553-1557 ◽  
Author(s):  
Sookhee Ha ◽  
Jiali Gao ◽  
Bruce Tidor ◽  
John W. Brady ◽  
Martin Karplus
Keyword(s):  
Free Energy ◽  
Solvent Effect ◽  
Simulation Analysis ◽  
Energy Simulation

Quantum Chemical and Free Energy Simulation Analysis of Retinal Conformational Energetics

1997 ◽  
Vol 37 (6) ◽  
pp. 1018-1024 ◽  
Author(s):  
Jérôme Baudry ◽  
Serge Crouzy ◽  
Benoît Roux ◽  
Jeremy C. Smith
Keyword(s):  
Free Energy ◽  
Quantum Chemical ◽  
Simulation Analysis ◽  
Energy Simulation

Determination of Base Flipping Free Energy Landscapes from Nonequilibrium Stratification

2019 ◽  
Author(s):  
Xiaohui Wang ◽  
Zhaoxi Sun
Keyword(s):  
Free Energy ◽  
Energy Landscape ◽  
Sampling Technique ◽  
Umbrella Sampling ◽  
Energy Simulation ◽  
Nonlinear Dependence ◽  
Free Energy Landscape ◽  
Convergence Criterion ◽  
Base Flipping ◽  
Convergence Behavior

<p>Correct calculation of the variation of free energy upon base flipping is crucial in understanding the dynamics of DNA systems. The free energy landscape along the flipping pathway gives the thermodynamic stability and the flexibility of base-paired states. Although numerous free energy simulations are performed in the base flipping cases, no theoretically rigorous nonequilibrium techniques are devised and employed to investigate the thermodynamics of base flipping. In the current work, we report a general nonequilibrium stratification scheme for efficient calculation of the free energy landscape of base flipping in DNA duplex. We carefully monitor the convergence behavior of the equilibrium sampling based free energy simulation and the nonequilibrium stratification and determine the empirical length of time blocks required for converged sampling. Comparison between the performances of equilibrium umbrella sampling and nonequilibrium stratification is given. The results show that nonequilibrium free energy simulation is able to give similar accuracy and efficiency compared with the equilibrium enhanced sampling technique in the base flipping cases. We further test a convergence criterion we previously proposed and it comes out that the convergence behavior determined by this criterion agrees with those given by the time-invariant behavior of PMF and the nonlinear dependence of standard deviation on the sample size. </p>

Kinetics of Ion-Pair Effect of Aquation of Bromopentaammine Cobalt(III) Complex in Different Dicarboxylate Media

2011 ◽  
Vol 324 ◽  
pp. 166-169 ◽  
Author(s):  
Farah Zeitouni ◽  
Gehan El-Subruiti ◽  
Ghassan Younes ◽  
Mohammad Amira
Keyword(s):  
Free Energy ◽  
Solvent Effect ◽  
Compensation Effect ◽  
Ion Pairing ◽  
Reaction Rates ◽  
Ion Pair ◽  
Free Energy Of Activation ◽  
Different Types ◽  
Different Temperatures ◽  
Kinetics Of

The rate of aquation of bromopentaammine cobalt(III) ion in the presence of different types of dicarboxylate solutions containing tert-butanol (40% V/V) have been measured spectrophotometrically at different temperatures (30-600°C) in the light of the effects of ion-pairing on reaction rates and mechanism. The thermodynamic and extrathermodynamic parameters of activation have been calculated and discussed in terms of solvent effect on the ion-pair aquation reaction. The free energy of activation ∆Gip* is more or less linearly varied among the studied dicarboxylate ion-pairing ligands indicating the presence of compensation effect between ∆Hip* and ∆Sip*. Comparing the kip values with respect of different buffers at 40% of ter-butanol is introduced.

Energy Consumption Analysis on Office Building Ventilation

2012 ◽  
Vol 516-517 ◽  
pp. 1139-1143
Author(s):  
Ke Chun Sun ◽  
Wei Jun Zhang
Keyword(s):  
Energy Consumption ◽  
Energy Saving ◽  
Air Conditioning ◽  
Room Temperature ◽  
Simulation Analysis ◽  
Simulation Software ◽  
Energy Simulation ◽  
Office Building ◽  
Saving Effect ◽  
Night Ventilation

Chongqing weather conditions as the representative, energy simulation software DesT-c Chongqing office building energy simulation analysis, simulated natural building under different ventilation conditions at room temperature, the energy consumption of building cooling load and air-conditioning system changes, with an emphasis on energy-saving effect of the night ventilation; The study showed that in Chongqing reasonable use of ventilation reduce building natural room temperature to a certain extent; Sensitive indicators of building air conditioning energy consumption than the heating energy consumption of ventilation was significantly; Night ventilation when the number of ventilators is less than 5 times / h, the energy saving effect is very significant.

Thermodynamic studies in solution. Part IV. Solvent effect on the solvolysis of tert-butyl chloride. A new treatment of the experimental data

1979 ◽  
Vol 57 (5) ◽  
pp. 500-502 ◽  
Author(s):  
Joaquim Jose Moura Ramos ◽  
Jacques Reisse ◽  
M. H. Abraham
Keyword(s):  
Free Energy ◽  
Solvent Effect ◽  
Free Energies ◽  
Butyl Chloride ◽  
Activation Free Energy ◽  
Tert Butyl ◽  
New Treatment ◽  
The One ◽  
Activated Complex ◽  
Tert Butyl Chloride

A new treatment of the solvent effect on the solvolysis of tert-butyl chloride is proposed. This treatment is based on activation free energy measurements and on transfer free energy measurements of the reactant (R) on the one hand and of a model (M) of the activated complex (AC) on the other hand. Solute–solvent interaction free energies for the reactant, the activated complex and the model compound are estimated. This estimation involves the calculation of the free energy of cavity formation of these various solutes (R, AC, and M) in all the solvents. These cavity terms, which are a function of the cohesive properties of the solvent and of the surface of the cavity do not reflect the electronic structure of the solute whereas the interaction free energy term does. The method we propose can be described as a new 'experimental' approach for the study of the charge separation in an activated complex.

A reaction density functional theory study of the solvent effect in prototype SN2 reactions in aqueous solution

2019 ◽  
Vol 21 (45) ◽  
pp. 24876-24883 ◽  
Author(s):  
Cheng Cai ◽  
Weiqiang Tang ◽  
Chongzhi Qiao ◽  
Peng Jiang ◽  
Changjie Lu ◽  
...  
Keyword(s):  
Aqueous Solution ◽  
Density Functional Theory ◽  
Free Energy ◽  
Solvent Effect ◽  
Density Functional ◽  
Density Functional Theory Study ◽  
Functional Theory ◽  
Sn2 Reactions ◽  
Energy Profiles ◽  
Free Energy Profiles

Reaction density functional theory (RxDFT), combining quantum DFT with classical DFT, has been employed to investigate the solvent effect and free energy profiles of SN2 reactions in aqueous solution.

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