열역학 물성 예측을 위한 분자 시뮬레이션 소프트웨어의 개발

장재언; Jaeeon Chang

Korean Chemical Engineering Research, Vol.49, No.3, 361-366, June, 2011

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열역학 물성 예측을 위한 분자 시뮬레이션 소프트웨어의 개발

Development of Molecular Simulation Software for the Prediction of Thermodynamic Properties

장재언^†

서울시립대학교 화학공학과, 130-743 서울시 동대문구 시립대길 13

Jaeeon Chang^†

Department of Chemical Engineering, University of Seoul, Siripdae-gil 13, Dongdaemun-gu, Seoul 130-743, Korea

E-mail:

초록

몬테칼로 시뮬레이션 방법을 사용하여 유기화합물의 열역학적 물성을 예측하는 새로운 분자 시뮬레이션 소프트웨어를 개발하였다. 분자 구조, 분자간 포텐셜 에너지 함수와 엄밀한 통계역학적 원리로부터 많은 분자들을 포함한 계의 거동에 대한 확률 분포를 구하고 거시적인 계의 열역학적 물성을 계산한다. 본 연구에서 개발된 소프트웨어 cheMC는 윈도우즈 플랫폼에 기반하여 사용자 접근성이 좋고, 가시화 도구 및 차트 생성 기능 등 직관적인 인터페이스로 시뮬레이션 관리가 쉽다. 분자 시뮬레이션은 기존의 상태 방정식을 사용한 열역학 물성 연구를 보완하고, 향후 그 역할이 점점 더 커질 것으로 기대된다.

By using Monte Carlo simulation method we developed a new molecular simulation software which can be used to predict the thermodynamic properties of organic compounds. Starting from molecular structure and intermolecular potential function, rigorous statistical mechanical principles give a probability distribution for the behavior of a system containing many molecules, which enables us to calculate macroscopic thermodynamic properties of the system. The software developed in this work, cheMC, is based on Windows platform providing with easy access. One can efficiently administrate simulations by using an intuitive interface equipped with visualization tool and chart generation. It is expected that molecular simulations supplement the equation of state approach and will play a more important role in the study of thermodynamic properties.

Keywords:Molecular Simulation;Monte Carlo;Thermodynamic Property;Chemical Potential;Expanded Ensemble

[References]

Sandler SI, Chemical, Biochemical and Engineering Thermodynamics 4th ed., John Wiley & Sons (2006)
Soave G, Chem. Eng. Sci., “Equilibrium Constants from a Modified Redlich-Kwong Equation of State”, 27, 1197 (1972)
Peng DY, Robinson DB, Ind. Eng. Chem. Fundam., “A New Two-Constant Equation of State", 15, 59 (1976)
Frenkel D, Smit B, Understanding Molecular Simulations 2nd ed., Academic (2002)
Case DA, Cheatham III, TE, Darden T, Gohlke H, Luo R, Merz Jr, KM, Onufriev A, Simmerling C, Wang B, Woods R, J. Comp. Chem., “The Amber Biomolecular Simulation Programs”, 26, 1668 (2005)
Brooks BR, Brooks III, CL, Mackerell AD, Nilsson L etc, J. Comp. Chem., “CHARMM: The Biomolecular Simulation Program", 30, 1545 (2009)
http://accelrys.com/products/materials-studio/.
http://campus.uos.ac.kr/chemc/chemc.htm.
Widom B, J. Chem. Phys., “Some Topics in the Theory of Fluids”, 39, 2808 (1963)
Lyubartsev AP, Martsinovski AA, Shevkunov SV, Vorontsov-Vel’yaminov PN, J. Chem. Phys., “New Approach to Monte Carlo Calculation of the Free Energy: Method of Expanded Ensembles", 96, 1776 (1992)
Lyubartsev AP, Laaksonen A, Vorontsov-Velyaminov PN, Mol. Phys., “Free Energy Calculations for Lennard-Jones Systems and Water Using the Expanded Ensemble Method. A Monte Carlo and Molecular Dynamics Simulation Study", 82, 455 (1994)
Lyubartsev AP, Jacobsson SP, Sundholm G, Laaksonen A, J. Phys. Chem. B, “Solubility of Organic Compounds in Water/Octanol Systems. A Expanded Ensemble Molecular Dynamics Simulation Study of log P Parameters", 105(32), 7775 (2001)
Errington JR, Boulougouris GC, Economou IG, Panagiotopoulos AZ, Theodorou DN, J. Phys. Chem. B, “Molecular Simulation of Phase Equilibria for Water-Methane and Water-Ethane Mixtures", 102(44), 8865 (1998)
Khare AA, Rutledge GC, J. Chem. Phys., “Chemical Potential of Model Benzene Fluids Using Expanded Ensemble Monte Carlo Simulations", 110(6), 3063 (1999)
Aberg KM, Lyubartsev AP, Jacobsson SP, Laaksonen A, J. Chem. Phys., “Determination of Solvation Free Energies by Adaptive Expanded Ensemble Molecular Dynamics", 120(8), 3770 (2004)
Chang J, Sandler SI, J. Chem. Phys., “Determination of Liquid-Solid Equilibria Using the Histogram Reweighting Method and Expanded Ensemble Simulation", 118(18), 8390 (2003)
Chang J, Lenhoff AM, Sandler SI, J. Chem. Phys., “Determination of Fluid-Solid Transitions in Model Protein Solutions Using the Histogram Reweighting Method and Expanded Ensemble Simulations", 120(6), 3003 (2004)
Chang J, Lenhoff AM, Sandler SI, J. Phys. Chem. B, “The Combined Simulation Approach of Atomistic and Continuum Models for the Thermodynamics of Lysozyme Crystals", 109(41), 19507 (2005)
Chang J, Sandler SI, J. Chem. Phys., “The Free Energies of Fullerene C60 Orientational Order-Disorder Phase Transition", 125, 054705 (2006)
Chang J, J. Chem. Phys., “The Calculation of Chemical Potential of Organic Solutes in Dense Liquid Phases by Using Expanded Ensemble Monte Carlo Simulations", 131, 074103 (2009)
http://www.opengl.org/.

[Referenced By]

[1] Sandler SI, Chemical, Biochemical and Engineering Thermodynamics 4th ed., John Wiley & Sons (2006)

[2] Soave G, Chem. Eng. Sci., “Equilibrium Constants from a Modified Redlich-Kwong Equation of State”, 27, 1197 (1972)

[3] Peng DY, Robinson DB, Ind. Eng. Chem. Fundam., “A New Two-Constant Equation of State", 15, 59 (1976)

[4] Frenkel D, Smit B, Understanding Molecular Simulations 2nd ed., Academic (2002)

[5] Case DA, Cheatham III, TE, Darden T, Gohlke H, Luo R, Merz Jr, KM, Onufriev A, Simmerling C, Wang B, Woods R, J. Comp. Chem., “The Amber Biomolecular Simulation Programs”, 26, 1668 (2005)

[6] Brooks BR, Brooks III, CL, Mackerell AD, Nilsson L etc, J. Comp. Chem., “CHARMM: The Biomolecular Simulation Program", 30, 1545 (2009)

[7] http://accelrys.com/products/materials-studio/.

[8] http://campus.uos.ac.kr/chemc/chemc.htm.

[9] Widom B, J. Chem. Phys., “Some Topics in the Theory of Fluids”, 39, 2808 (1963)

[10] Lyubartsev AP, Martsinovski AA, Shevkunov SV, Vorontsov-Vel’yaminov PN, J. Chem. Phys., “New Approach to Monte Carlo Calculation of the Free Energy: Method of Expanded Ensembles", 96, 1776 (1992)

[11] Lyubartsev AP, Laaksonen A, Vorontsov-Velyaminov PN, Mol. Phys., “Free Energy Calculations for Lennard-Jones Systems and Water Using the Expanded Ensemble Method. A Monte Carlo and Molecular Dynamics Simulation Study", 82, 455 (1994)

[12] Lyubartsev AP, Jacobsson SP, Sundholm G, Laaksonen A, J. Phys. Chem. B, “Solubility of Organic Compounds in Water/Octanol Systems. A Expanded Ensemble Molecular Dynamics Simulation Study of log P Parameters", 105(32), 7775 (2001)

[13] Errington JR, Boulougouris GC, Economou IG, Panagiotopoulos AZ, Theodorou DN, J. Phys. Chem. B, “Molecular Simulation of Phase Equilibria for Water-Methane and Water-Ethane Mixtures", 102(44), 8865 (1998)

[14] Khare AA, Rutledge GC, J. Chem. Phys., “Chemical Potential of Model Benzene Fluids Using Expanded Ensemble Monte Carlo Simulations", 110(6), 3063 (1999)

[15] Aberg KM, Lyubartsev AP, Jacobsson SP, Laaksonen A, J. Chem. Phys., “Determination of Solvation Free Energies by Adaptive Expanded Ensemble Molecular Dynamics", 120(8), 3770 (2004)

[16] Chang J, Sandler SI, J. Chem. Phys., “Determination of Liquid-Solid Equilibria Using the Histogram Reweighting Method and Expanded Ensemble Simulation", 118(18), 8390 (2003)

[17] Chang J, Lenhoff AM, Sandler SI, J. Chem. Phys., “Determination of Fluid-Solid Transitions in Model Protein Solutions Using the Histogram Reweighting Method and Expanded Ensemble Simulations", 120(6), 3003 (2004)

[18] Chang J, Lenhoff AM, Sandler SI, J. Phys. Chem. B, “The Combined Simulation Approach of Atomistic and Continuum Models for the Thermodynamics of Lysozyme Crystals", 109(41), 19507 (2005)

[19] Chang J, Sandler SI, J. Chem. Phys., “The Free Energies of Fullerene C60 Orientational Order-Disorder Phase Transition", 125, 054705 (2006)

[20] Chang J, J. Chem. Phys., “The Calculation of Chemical Potential of Organic Solutes in Dense Liquid Phases by Using Expanded Ensemble Monte Carlo Simulations", 131, 074103 (2009)

[21] http://www.opengl.org/.