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

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

Prediction of Alkanolamine pKa Values by Combined Molecular Dynamics Free Energy Simulations and ab initio Calculations

2019 ◽  
Author(s):  
Javad Noroozi ◽  
William Smith
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Ab Initio Calculations ◽  
Gas Phase ◽  
Quantum Chemical ◽  
Phase Reaction ◽  
Pka Values ◽  
Gas Phase Reaction ◽  
Reaction Free Energy ◽  
Energy Simulations

We use molecular dynamics free energy simulations in conjunction with quantum chemical calculations of gas phase reaction free energy to predict alkanolamines pka values. <br>

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>

scholarly journals Thermodynamic Parameters of PbTe Crystals: DFT-Calculations

2015 ◽  
Vol 16 (1) ◽  
pp. 28-33
Author(s):  
D. M. Freik ◽  
B. P. Volochanska ◽  
T. O. Parashchuk
Keyword(s):  
Density Functional Theory ◽  
Free Energy ◽  
Electronic Structure ◽  
Thermodynamic Parameters ◽  
Quantum Chemical ◽  
Density Functional ◽  
Cubic Phase ◽  
Functional Theory ◽  
Temperature Dependences ◽  
Analytical Expressions

Based on the analysis of the crystal NaCl type and electronic structure of cubic phase CdS crystals the cluster models have been built for calculation of the geometric and thermodynamic parameters. According to density functional theory (DFT) and using the hybrid valence base set B3LYP the temperature dependence of the energy ΔE and the enthalpy ΔH of formation, Gibbs free energy ΔG, entropy ΔS, specific heat at constant volume CV and pressure CP of the crystals have been found. The analytical expressions of the temperature dependences of presented thermodynamic parameters which was approximated from the quantum- chemical calculations data and with using mathematical package Maple 14 have been received.

scholarly journals Quantum-chemical calculation free energy of vinpocetine molecule release from sodium alginate

2018 ◽  
Vol 22 (1) ◽  
pp. 116-123
Author(s):  
Yuliya Polkovnikova ◽  
Kseniya Korynova ◽  
Amila Jeewantha Halahakoon
Keyword(s):  
Free Energy ◽  
Sodium Alginate ◽  
Quantum Chemical Calculation ◽  
Quantum Chemical ◽  
Chemical Calculation

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.

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