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  3. Gibbs free energy calculations for guest exchange in sI gas hydrates using molecular dynamics simulations

Gibbs free energy calculations for guest exchange in sI gas hydrates using molecular dynamics simulations

Number of pages: 136 File Format: word File Code: 31855
Year: 2014 University Degree: Master's degree Category: Physics
Tags/Keywords: Compressibility coefficient - free energy - Gas hydrate - Gibbs free energy - Hydrate - Linear thermal expansion - methane - sI gas hydrate - Solid host compounds
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  • Summary of Gibbs free energy calculations for guest exchange in sI gas hydrates using molecular dynamics simulations

    Dissertation for Master Degree

    Physical Chemistry

    Abstract

    Gas hydrates are a group of solid host compounds that play an important role in several processes such as gas storage, transfer and separation, heterogeneous catalysis and water purification. These crystals are formed at a temperature higher than the freezing point of water and high pressure. There are different methods to calculate the free energy difference: 1) Disruption 2) Gradual 3) Thermodynamic integration, in this research, the thermodynamic integration method is used to calculate the free energy difference of different processes of substituting hydrogen sulfide guest instead of methane guest in large and small shelves of sI gas hydrate. In the calculation of the free energy difference using the thermodynamic integration method for these processes, separate van der Waals and electrostatic contributions have been calculated. Also, the structural properties that include the radial distribution function, volume temperature dependence, linear thermal expansion coefficient and isothermal compressibility coefficient, sI methane gas hydrate and different binary sI gas hydrates (methane + hydrogen sulfide) have been investigated. Gas molecules are surrounded by water molecules. There are many gases that have a suitable structure for the formation of hydrates, such as carbon dioxide, hydrogen sulfide, and hydrocarbons with low carbon numbers. For more than 70 years, gas hydrates have been raised as a problem in gas transmission lines. Therefore, most of the primary research in this field is related to the operational conditions of hydrate formation and the effect of using inhibitory substances in preventing its formation. Today, paying attention to the gas hydrate phenomenon and its useful and practical aspects shows the necessity of conducting more research in this field. Since several decades ago, it has been proven that there are huge amounts of natural gas stored in gas hydrates in the ocean floor and polar regions. It is estimated that each cubic meter of hydrate contains more than 170 cubic meters of methane gas in standard conditions[1].

    Given the limited resources of fossil fuels, the exploration of gas hydrate sources for energy supply may be considered in the future. The great ability of gas hydrate in natural gas storage makes it attractive to use it for storage and transportation purposes of natural gas and other gases as a competitor to liquefaction and condensing methods. Gas hydrates can also be used in separation processes. Gas hydrates can only be formed with a limited number of substances. If we intend to separate a substance from a mixture, we can use the ability to form or not form its hydrate or other substances in the salt mixture. For example, we can refer to the provision of drinking water or the separation of gas flows. Unfortunately, there are concerns about the stability of natural gas hydrate reserves under changing pressure and temperature conditions. According to some researchers, when the global temperature increases due to the phenomenon of greenhouses, it is possible that the hydrates become unstable and break down, and as a result, large amounts of gas enter the atmosphere and intensify the effect of the greenhouse phenomenon.

    The conditions necessary for the formation of hydrates include the right temperature, pressure, the presence of water molecules, and the presence of gas molecules.

    Gas hydrates act as hosts for water molecules and accommodate gas molecules inside their cavity. All gas molecules are not able to form hydrates, and only molecules that are non-polar or have low polarity and are small in size and can fit in these holes are able to form hydrates.

     

    1-2- Gas hydrates over time

    The history of gas hydrate is divided into three main periods:

    The first period: this period began since its discovery in 1810 and continues until now. It is related to the interesting phenomenon of gas hydrate formation from the scientific point of view, because the accumulation of water and gas in a solid phase (hydrate) is significant from the point of view of science.

    The second period: It started almost from 1934 with the statement that the formation of hydrate causes clogging of natural gas transmission lines, and it continues until now. In this period, hydrate is mainly considered as a problem for natural gas producers.

    Third period: It is related to the discovery of natural gas hydrate reserves. The existence of gas hydrates in nature was proved by Makogon[2] in the 1960s, after which many efforts were made to discover and develop hydrate reserves. Undoubtedly, the problems facing the production of huge reserves of gas hydrates is one of the most important challenges of the energy industry in the 21st century. The first commercial production of natural gas hydrate deposits happened in Siberia

    Abstract

    Clathrate Hydrates are the group of solid host compounds that they are important in multiple (different) processes such as accumulation, transition and gas separation and catalyz heterogeneous and water treatment. These crystals are composed in temperatures above freezing point. There are different (various) methods to compute free energy difference: 1) Disorder (derangement) 2) gradual 3) thermodynamic intergtation.

    In this study is used thermodynamic integration to compute free energy difference instead of guest methane in big and small shelves town Gas Hydrates sI. To compute free energy by thermodynamic integration, Computed share separate Vandrvals and Electrostatic.

    Also structural properties include the radial distribution function, the temperature dependence of content, the coefficient of linear thermal expansion, iso thermal compressibility factor, methane gas hydrate SI, various binary hydrates sI, (Mathan + Hydrogen solidified) is checked.

  • Contents & References of Gibbs free energy calculations for guest exchange in sI gas hydrates using molecular dynamics simulations

    List:

    Chapter One: Gas hydrate

    1-1- Gas hydrate. 2

    1-2- Gas hydrates over time. 3

    1-3- The structure of gas hydrates. 4

    1-3-1- sI structure 5

    1-3-2- sII structure 6

    1-3-3- sH structure. 6

    1-3-4- Notes on hydrate structures. 7

    1-4- Specifications of the guest molecule. 8

    1-5- Gas hydrates in nature. 8

    1-6- The importance of gas hydrates. 10

    1-6-1- Benefits of gas hydrate. 11

    1-6-1-1- Transmission of natural gas. 11

    1-6-1-2- source of energy. 12

    1-6-1-3- carbon dioxide separation. 12

    1-6-1-4- gas hydrates in the food industry. 13

    1-6-1-4-1- Concentrating fruit juices 13

    1-6-1-4-2- Sweetening of sea water 13

    1-6-1-4-3- Separation of enzymes 14

    1-6-2- Harms of gas hydrate. 14

    1-7- Inhibitors 15

    1-7-1- Thermodynamic inhibitors. 15

    1-7-2- non-thermodynamic inhibitors. 16

    1-7-3- Inhibitory criteria. 16

    1-8- absorption. 17

    Chapter Two: Molecular Dynamics Simulation

    2-1- History of simulation. 20

    2-2- Molecular dynamics simulation. 21

    2-3- Model systems and interaction potentials. 21

    2-4- Introducing the potential model for the interaction between the constituent molecules of the system. 23

    2-5- Introducing the potential model for the interaction between the system and the environment. 23

    2-5-1- Boundary conditions of rounds. 24

    2-5-2- Cutting the potential and contracting the closest image. 25

    2-6- Time integration algorithm. 25

    2-6-1- Verle's algorithm. 26

    2-6-2- Verle's leap algorithm. 27

    2-6-3- Velocity Verlet Algorithm. 28

    2-7- The first step in molecular dynamics simulation. 29

    2-7-1- Determining the initial locations of particles. 29

    2-7-2- Determining the initial speeds of particles. 30

    2-8- The second step in molecular dynamics simulation. 30

    2-9- The third step in molecular dynamics simulation is measuring thermodynamic properties. 31

    2-10- The fourth step in molecular dynamics simulation: analysis of results. 32

    2-11- Types of sets in molecular dynamics simulation. 32

    2-12- Types of errors in molecular dynamics simulation. 33

    2-12-1- Statistical errors. 33

    2-12-2- Systematic errors. 33

    2-13- Limitations of molecular dynamics simulation. 34

    2-13-1- Quantum effects. 34

    2-13-2- Determination of interaction potentials. 34

    Chapter three: Gibbs free energy calculations

    3-1- Types of thermodynamic properties. 36

    3-1-1- Simple thermodynamic functions. 36

    3-1-1-1- Internal energy. 36

    3-1-1-2- Pressure. 37

    3-1-1-3- average square of force. 37

    3-1-2- Thermodynamic functions of the answer. 38

    3-1-3- entropy dependent properties. 39

    3-1-3-1- Thermodynamic integration. 40

    3-1-3-2- experimental particle method. 40

    3-1-4- free energy. 41

    3-2- Types of methods to calculate the difference of free energy. 43

    3-2-1- Thermodynamic disorder. 43 3-2-1-1- Calculation of the free energy difference of nitrogenous bases by thermodynamic disorder method 46

    3-2-2- Gradual method. 50

    3-2-3- multi-stage trajectory. 50

    3-2-4- thermodynamic integration. 53

    3-3- Application of free energy difference calculation methods. 53

    3-3-1- Thermodynamic cycles. 53

    3-3-2- Calculation of absolute free energy. 55

    Chapter 4: Gibbs free energy calculations for guest exchange in sI gas hydrate using molecular dynamics simulation

    4-1- Thermodynamic integration method. 58

    4-2- Research record. 59

    4-3- Characteristics of hydrogen sulfide molecule. 67

    4-4- Simulation software and input files in this research. 68

    4-4-1- Software input files. 68

    4-4-1-1- Initial particle structure file (CONFIG) 69

    4-4-1-2- Simulation control parameters determination file (CONTROL) 71

    4-4-1-3- Preparation of input file (FIELD) 72

    4-4-2- Software output files. 73

    4-4-2-1- Particles final structure file (REVCON)73

    4-4-2-1- The final particle structure file (REVCON) 74

    4-4-2-2- The main output file of the simulation (OUTPUT) 74

    4-4-2-3- The information file of the simulation process in machine language (REVIVE) 74

    4-5- Calculation of the free energy of different substitutions of hydrogen sulfide instead of methane in gas hydrates sI 75

    4-6- Calculation of structural and thermodynamic properties. 83

    4-6-1- Radial distribution function. 84

    4-6-2- Examining the dependence of unit cell volume on temperature 92

    4-6-3- Examining the coefficient of linear thermal expansion. 97

    4-6-4- Investigating isothermal compressibility coefficient 105

    References. 109

    Source:

     

     

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    [3] Solan, E. D.; and Koh, C. A.; Clathrate Hydrates of Natural Gases, 3rd. Edition, CRC Press, 2008.

    [4] Van der Waals, J. H.; and Platteeuw, J. C.; Clathrate Solution, Adv, Chem. Phy. 1959, 2, 1. [5] Redger, P. M. Mechanisms for Stabilizing Water Clathrates, 1990, 5, 315.                     

    [6] Stakelberg, V. M.; J. Naturwiss. 1949, 36, 359. [7] Jeffry, G.; A. Mcmullan, R.; K. J. Prog. Inorg. Chem. 1967, 8, 43.

    [8] Jeffry, G.; A. Inclusion Compounds, Academic Press. 1984.135.

    [9] Yakushev, V. International Conference on Gas Hydrate, 4th Ed. Yokohama, 2002. [10] Gudmun dsson, J. S.;  Parlaktuna, M.;  Khokhare, A. A. J. SPE Production & Facilities. 1994, 69. [11] Chatti, I.; Delahaye, A.; Fournaison. L.; Petitet, J. P. J. Energy Conversion and Management.  2005, 46, 1333.

    [12] Javanmardi, J.; Moshfeghian, M. J. Energy Fuels. 1998, 12, 219. [13] Nagahama, N. J. Food Phase Equilibria. 1996, 116, 126.

    [14] Solan, E. D. Clathrate Hydrates of Natural Gases. Marcel Decker, Inc. New York. 1998, 59. [15] Chanyu, S.;  Wenzhi, L.; Xin, Y.; Fengguang Qing, Y.; Liang, M.; Jun, C.; Bie, L.; Guangjin, G. J. Chemical Engineering. 2011, 19,151. [16] Keith, A. Kvenvolden, U.S. Geological Survey Menlo Park, Gas Hydrates Geological Perspective and Global Change. 1993, 173. [17] Jalili, S., Molecular Dynamics Simulation, Ferdowsi University Press, Mashhad, 1385. [18] Alder, B.J.; Wainwright, T.E. J.Chem. Phys. 1957, 27,1208.

    [19] Alder, B.J.; Wainwright, T.E. J.Chem. Phys. 1959, 31, 459.

    [20] Rahman, A. Phys. Rev. 1964, 136A, 405.

    [21] McCammon, J. A.; Gelin, B. R.; Karplus, M. Nature. 1977, 207, 585.

    [22] Goharshadi, A., Mousavi, M., Mousavi, F., Mursali, A., Fundamentals of Molecular Dynamics Simulation, Ferdowsi University Press, Mashhad, 1385.

    [23] Norbert, A.; Kurrt, B.;  Helmut G.; Kurt, K. John von Nevmann Institute for Computing. 2004, 23,1.

    [24] Jarsaw, M. Cornell University, Ithaca, New York, USA Nicholas University, Tourn, Poland, 2010.

    [25] Jennifer, L.; Miller and Peter A. Kollman. Solvation Free Energies of the Nucleic Acid Bases. J. Phy.Chem.1996, 100, 8587.

    [26] Lu, N. D.; Kofke, A. Accuracy of Free Energy Perturbation Calculation in Molecular Simulation I. J.Chem. Phys. 2001, 114, 7303.

    [27] Lu, N. D.; Kofke, A. Accuracy of Free Energy Perturbation Calculation in Molecular Simulation II. J.Chem. Phys. 2001, 115, 6866. [28] Florian, J.; Goodman. M. F. and Warshel. Free Energy Perturbation Calculation of DNA Destabilization by Base Substitution the Effect of Neutral Guanine Thymine, Adenine Cytosine & Adenine difluorotoluene Mismatches.J.Phys.Chem.B. 2000,104, 10092.

    [29] Brandsdal, B.O.; and Smalas.O. A. Evaluation of protein association energies by free energy perturbation. Protein Eng. 2000, 13, 239. [30] Straatama, T. P.; and McCammon .A. Computational Alchemy Annu. Rev.Phys.Chem. 1992, 43, 431. [31] Beveridege, D.

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