Molecular Dynamics Simulation of Methane Hydrate Growth in the

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Molecular Dynamics Simulation of Methane Hydrate Growth in the Presence of the Natural Product Pectin Ping Xu, Xuemei Lang, Shuanshi Fan, Yanhong Wang, and Jun Chen J. Phys. Chem. C, Just Accepted Manuscript • DOI: 10.1021/acs.jpcc.5b10342 • Publication Date (Web): 22 Feb 2016 Downloaded from http://pubs.acs.org on February 23, 2016

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The Journal of Physical Chemistry

Molecular Dynamics Simulation of Methane Hydrate Growth in the Presence of the Natural Product Pectin Ping Xu; Xuemei Lang; Shuanshi Fan; Yanhong Wang*; Jun Chen Key Lab of Enhanced Heat Transfer and Energy Conservation, Ministry Education, School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510640, China * Corresponding Author: Yanhong Wang*.

Tel: + 86-20-22236581,

wyh@ scut.edu.cn

ACS Paragon Plus Environment

E-mail:


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ABSTRACT. Molecules dynamics simulation was used to examine the growth of methane hydrate in the presence of natural products pectin at different concentrations, including the mass fraction 2.46%, 3.62%. Snapshots of the system configurations with time, radial distribution functions of the carbon atoms and the total energy of the system were employed to characterize the effect of pectin on methane hydrate growth. Results indicated that pectin is a good inhibitor of methane hydrate. The higher the concentration of pectin is, the better the effect of inhibition is. The double-bonded oxygen atoms of pectin combine with hydrogen atoms of water, and the hydrogen atoms of hydroxyl in pectin combine with oxygen atoms of water through hydrogen bonds which disturbed the further growth of the methane hydrate. The role of the pectin's active groups in hydrogen bonds with water both as proton donor and electron acceptor, this makes pectin has a better inhibitory effect on growth of methane hydrate. Keywords.

molecular simulation,

methane hydrate,

inhibitor,


pectin

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1 Introduction Clathrate hydrate are nonstoichiometric crystalline composed of guest molecules and water molecules. The host molecules inform different kinds of cage by hydrogen bonds. The guest molecules, such as CH4, C2H6, CO2, H2S, etc, occupy the cavities at high-pressure and low-temperature1. Clathrate hydrate can easily form in pipelines in the oil and gas transport and production, which is a serious threat for oil and gas industry. The frequently used methods to prevent the formation of hydrate were injecting thermal hydrate inhibitors (THIs) or kinetic hydrate inhibitor (KHIs). THIs, such as methanol, glycol, were used with high concentrations (30%-60%), which lead to high cost and environmental pollution. KHIs are active in low dosage, but its effctive subcooling is less than 10 K and its degradability is poor. Therefore, it is necessary to develop new KHIs, which are efficient at higher sub-cooling and environmental friendly. Testing of the new KHIs involves experiments at high pressures with high cost and time consumption, but the computer simulation is cheap, universal and powerful, molecular dynamic (MD) simulation can be as a valuable research tool. So far, MD simulation has been employed to investigate the formation and growth2-5, dissociation6-8, and inhibition mechanisms9-11 of gas hydrate at the molecular scale. There are few researchers develop the natural inhibitor, for example chitosan12, tapioca13-14, amino acid15-17, antifreeze protein18-21. These natural products have some effects on the hydrate inhibitions. Antifreeze proteins showed higher activities in inhibiting information THF hydrate than PVP, and also have the ability to eliminate



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the memory effect18-21. Chitosan and cationic starches are good inhibitors, the induction time of gas hydrate formation evidently increased with them12-14. However, few researches investigated the inhibition mechanism of these natural products. In this paper, we used a natural product, pectin, as the methane hydrate inhibitor and studied the inhibition mechanism of pectin in the growth of CH4 hydrate by molecular dynamics simulations. Pectin is a nontoxic, polysaccharide natural product. It is a new KHI in gas hydrate applications. Figure 1 shows the pectin structure. 2 Simulation Details The methane hydrate formation and growth system consist of methane/water solution and a solid hydrate crystal, the simulation box size is 2.376×2.376 ×4.752 nm, as shown in Figure 2 (a). The liquid phase contains 64 methane molecules and 368 water molecules, and the crystal hydrate phase consist of a 2×2×2 unit cell of structure I(sI). The pectin system was added the pectin to the liquid phase and the liquid-solid interface, as demonstrated in Figure 2 (b), (c) and Figure 3. The insertion process caused some methane or water molecules overlapped with inhibitor which were removed. The simulations were performed for both the without pectin and pectin systems, respectively. Dimer pectin in the concentrations 2.46% and trimer pectin in the concentrations 3.62% were added to study the effect on the formation and growth methane hydrate. The initially created model was build after the following steps. First, the model was performed by energy-minimized; then, a NVT simulation at 260 K with 30 ps to relax any extra stress; finally, NPT simulation was employed at 260 k


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and 15 MPa for 30 ps. After these optimized, the final configuration was achieved, which was used as the starting point for hydrate growth. NPT molecular dynamics simulation run for 20 ns at pressure P=15 MPa and temperature T=260 K, which temperature is above the ice melting point of TIP4P/2005 water (around 252 K22-24). Snapshots, radial distribution function (RDF) and potential energy were used to investigate the influence of pectin on methane hydrate. The crystalline hydrate was created following the Bernal-Fowler ice rules, the oxygen atoms in hydrate lattice were obtained from X-ray diffraction experiment25, and the hydrogen atoms were then added in a random manner. The TIP4P/2005 for water26, united atom Lennard-Jones for methane27 and gromos53a6 force field for pectin was set to describe the interactions within the molecular model. All the molecular dynamic simulations were performed using the open source package, GROMACS28. The periodic boundary condition was applied to the simulation box in all three directions and the long-range interaction was calculated using the particle mesh Ewald method with a Fourier spacing of 0.12 nm. The short-range interaction truncated at 10 Å. Bonds interactions involving H-atoms were constrained using the lincs algorithm. The Nose-Hoover29 temperature thermostat with a relaxation time of 2 ps and pressure Parrinello-Rahman30 with the relation time of 4 ps are used. The integration time is set to 2 fs. 3 Results and Discussion 3.1 Snapshots of the system configurations Snapshots of methane hydrate growth without or with pectin at 0 ns, 1 ns, 2 ns, 3



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ns, 4 ns, 5 ns, 10 ns, 20 ns are presented in Figure 4-6. One water molecule was marked during the simulation. Figure 4 was snapshots of the methane hydrate growth without pectin system. At 1 ns, the water molecule tend to be ordered at the liquid-solid interface, which implied the methane hydrate began to grow. At this moment, the water molecules far away the liquid-solid interface were still in disordering. With the time increased, the ordered water molecules were more and more. At 3 ns, most of the water and methane molecules have formed gas hydrate. The marked water molecule involved in a cage and fixed at the site. Figure 5 (a) and (b) displayed the snapshot configuration of simulation with 2.46% and 3.62% of pectin in the aqueous solution system, respectively. Since the presence of the pectin, there appeared the methane gas gathered, gas and liquid phase splitting obviously at 1 ns and 2 ns. The same phenomenon appeared in 3.62% pectin system. This made the pectin form a layer between water and guest molecules, which increased the mass transfer resistance and resulted in the difficulties of the hydrate growth31-32. In the simulation system of 2.46% pectin, there were no apparent hydrate growth in 1 ns, and a few new hydrate appeared at the liquid-solid interface from 2 ns. At 4 ns, the marked water molecule has involved in a cage. Until 5 ns, the 2.46% of pectin system has formed the neat hydrogen bond network between H2O molecules. While in the 3.62% pectin system, methane hydrate emerge the growth at 5 ns. Most gas and water did not get rid of disorder until 20 ns. At 20 ns, the marked water interacts with pectin through H-bonds, which disturbed the H-bonds network among H2O molecules and prevented the further growth of gas hydrate (amplification figure in Figure 5 (b), 20


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ns). From the above, it is illustrated that the rate of growth in methane hydrate without pectin is faster than that with pectin. The higher concentrations of pectin, the slower growth rate of hydrate. Snapshots of methane hydrate growth with pectin at the liquid-solid interface at 0 ns, 1 ns, 2 ns, 3 ns, 4 ns, 5 ns, 10 ns, 20 ns are presented in Figure 6. At the same time, the 3.62 % concentrations of pectin performed better inhibiting ability than 2.46 % pectin. The pectin at the liquid-solid interface system also exhibited the similar phenomenon to the pectin in aqueous solution about methane bubbles. At the beginning, pectin bound to interface by H-bonds, after few ns pectin moved to the gas-liquid interface. As the pectin stay in the interface, it bound to the water in hydrate by H-bonds. Inhibitor engaged in cage and retarded growth process. While the pectin interacted with liquid water molecules, which disrupted the neat H-bonds network between H2O molecules and prevented the gas hydrate growth. The Figure 7 show how pectin interacts with water molecules in detail. It is observed that the double-bonded oxygen atoms of pectin combined with hydrogen atoms of water, as well as the hydrogen atoms of hydroxyl in pectin combine with oxygen atoms of water through hydrogen bonds. The double-bonded oxygen atoms of pectin with high charge density can attract the hydrogen atoms of water. The hydroxyl of pectin with a small polarity provides a hydrogen atom, which form H-bonds with oxygen atoms of water. Additionally, there is a few H-bonds formed by the oxygen atoms of hydroxyl with hydrogen atoms of water (Figure 7). In order to examine the interaction between water and pectin, the RDF on oxygen in pectin (Op) and oxygen



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atoms in water molecules (Ow) was calculated and shown in Figure 8. The plot of the Op-Ow did show some close contact peak at 0.27 Å, the distance between two H-bonded oxygen atom, as that for Ow-Ow. This indicated that the oxygen atoms in pectin did play a role in the control of hydrate growth31. During the 20 ns simulation, we found the pectin molecules was more likely to stay at the interface between water and gas molecules, and active groups of pectin were easily to form more than one hydrogen bonds with water in hydrate and solution at appropriate conditions. The pectin layer in the interface of gas-liquid increased the mass transfer resistance. Pectin molecules disturbed the order between water molecules and the gas, and further formed H-bonds with water molecules, which disrupted the neat H-bonds network between H2O molecules and prevented the gas hydrate growth31, 33. These two functions make the pectin possess the kinetic inhibitor effects. 3.2 Radial distribution function of carbon atoms Radial distribution function can be interpreted as a ratio of the system area density to average density. RDF shows the probability of finding the same kinds of molecule from reference molecule. Dynamics calculation method of radial distribution function is the formulation (1):

1 g r   4r 2r

  N r  r  r  T

N

t 1

j 1

N T

(1)

Where N is the total number of molecular; T is the computer the total time; r is the distance difference; N is the number of molecules in between the r  r  r .


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From Figure 9, it can be seen that RDFs of carbon atoms distances between methane molecules were calculated at temperature T=260 K. There are three typical peaks at distances of 0.4 nm, 0.65 and 1.05 nm, which are methane molecules solvated in water, and methane was separated by the hydrate cage, respectively. For the without pectin system, shown in Figure 9 (a), peaks at 0.4 nm were decreasing as time forward, indicating the number of dissolved methane molecules decrease. The two typical peaks at 0.65 and 1.05 nm are increasing, indicating the growing number of CH4 molecules separated by the hydrate cage. Thus, the gas hydrate was growing with time. After 3 ns, the growth of hydrate has been completely, which is the reason why the peak of RDF at 10 ns and 20 ns was almost overlapped. The same trends were presented in the pectin concentrations of 2.46% system in Figure 9 (b). The characteristic peaks value at 0.65 and 1.05 nm in RDF for hydrate crystals was similar with non-pectin system in variation and the height of peaks. In the system of 3.62% pectin, the heights of 0.65 and 1.05 nm peaks are obviously lower than that of other two system at the same time, which means the methane hydrate amounts is less than the non-pectin and 2.46% of pectin system. 3.3 Total-energy of the system Total-energy of system provides a description of the thermodynamic properties of methane hydrate system. All systems initially contained a slab of hydrate crystallite, but they have different growth rate. Figure 10 showed the variation of the total energy with time for the non-pectin and pectin in the aqueous solution and at the liquid-solid interface systems. Initially,



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the energy of the system decreased steadily, after that these systems reached to the equilibrium state, the energy value remain unchanged. In the non-pectin system, the energy decreased rapidly. The system reached to the equilibrium state at about 2500 ps, which indicated that all the methane encaged in the hydrate cage and the perfect CH4 hydrate crystal structures were formed. The concentrations of 2.46% pectin in aqueous solution system reached to the equilibrium state at 5500 ps, pectin at the liquid-solid interface system at 6000 ps, the energy value decreased to about -35400 KJ/mol, during the rest of simulation time, the energy maintained a constant. While the concentrations of 3.62% in aqueous solution system reached to the equilibrium state at 13000 ps, pectin at the liquid-solid interface system at 14000 ps, the energy value dropped to about -33500 KJ/mol slowly and then remained a constant. The time of methane hydrate growth is prolonged above 5 times than non-pectin system, which indicates the pectin is a good kinetic inhibitor of methane hydrate. 4 Conclusions The effect of pectin on methane hydrate growth was studied on molecular dynamic simulation. The simulation results such as snapshots of the trajectory conformation, RDF of carbon atom and the total energy of the system showed that pectin is a good low dosage hydrate inhibitor. Within a certain concentration, higher concentration of pectin gives a better inhibition effect on methane hydrate growth. The pectin interacted with water molecules in hydrate and liquid. During the methane hydrate growth, the pectin formed a layer between water and guest molecules, which increased the mass transfer resistance and led to the difficulties of the growth. The


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double-bonded oxygen atoms and the hydrogen atoms of hydroxyl in pectin combined with hydrogen atoms and oxygen atoms in the water respectively, and form hydrogen bonds. These H-bonds disrupted the perfect cages of the hydrate and prevented the further growth of gas hydrate. ACKNOWLEDGEMENT This work was supported by the National Natural Science Foundation of China (51576069), the Fundamental Research Funds for the Central University (2015ZZ076), and China Postdoctoral Science Foundation (2015M572321)



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232, 901-901.


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FIGURE CAPTIONS Fig 1. Structure of pectin Fig 2. Initial configurations of (a) non-pectin system (b) 2.46% of pectin in the aqueous solution system (c) 3.62% of pectin in the aqueous solution system. The model consists of a 2 ×2 ×2 structure I hydrate slab (bottom), the liquid solution slabs (upper), water molecules are shown in blue, H-bonds in blue dotted line, methane in green, pectin in red. Fig 3. Initial configurations of 2.46% of pectin (left) and 3.62% of pectin (right) at the liquid-solid interface system. Fig 4. Snapshot configurations of 2.46% of pectin system at 0, 1, 2, 3, 4, 5, 10, 20 ns Fig 5. Snapshot configurations of (a) 2.46% of pectin (b) 3.62% of pectin in the aqueous solution system at 0, 1, 2, 3, 4, 5, 10, 20 ns. Fig 6. Snapshot configurations of (a) 2.46% of pectin (b) 3.62% of pectin at the liquid-solid interface system at 0, 1, 2, 3, 4, 5, 10, 20 ns Fig 7. The local amplification figure of pectin system. Three blue water molecules are shown in ball-stick, active groups of pectin in white Fig 8. Radial distribution functions for the oxygen atoms in water (Ow) and oxygen (Op) of the pectin Fig 9. Radial distribution functions of carbon atoms of CH4 hydrate at different simulation time with pectin concentrations. (a) non-pectin system (b) 2.46% of pectin system (c) 3.62% of pectin system Fig 10. The variation of the total energy with time for different system.



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FIGURE

Fig 1. Structure of pectin


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Fig 2. Initial configurations of (a) non-pectin system (b) 2.46% of pectin in the aqueous solution system (c) 3.62% of pectin in the aqueous solution system. The model consists of a 2 ×2 ×2 structure I hydrate slab (bottom), the liquid solution slabs (upper), water molecules are shown in blue, H-bonds in blue dotted line, methane in green, pectin in red.



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Fig 3. Initial configurations of 2.46% of pectin (left) and 3.62% of pectin (right) at the liquid-solid interface system.


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Fig 4. Snapshot configurations of non-pectin system at 0, 1, 2, 3, 4, 5, 10, 20 ns



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(a) 2.46% of pectin system


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(b) 3.62% of pectin system Fig 5. Snapshot configurations of (a) 2.46% of pectin (b) 3.62% of pectin in the aqueous solution system at 0, 1, 2, 3, 4, 5, 10, 20 ns.



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

(a) 2.46% of pectin system


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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


(b) 3.62% of pectin system Fig 6. Snapshot configurations of (a) 2.46% of pectin (b) 3.62% of pectin at the liquid-solid interface system at 0, 1, 2, 3, 4, 5, 10, 20 ns.



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Fig 7. The local amplification figure of pectin system. Three blue water molecules are shown in ball-stick, active groups of pectin in white


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6

Ow-Ow Op-Ow 4

gC-C

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


2

0 0.0

0.2

0.4

0.6

0.8

1.0

1.2

r(nm)

Fig 8. Radial distribution functions for the oxygen atoms in water (Ow) and oxygen (Op) of the pectin



3 1ns 10ns 20ns

gc-c

2

1

0 0.2

0.4

0.6

0.8

1.0

1.2

r(nm)

(a) non-pectin system 3

3

In the aqueous solution

1ns 10ns 20ns

At the liquid-solid interface 1ns 10ns 20ns

2

gC-C

gC-C

2

1

1

0 0.2

0.4

0.6

r(nm)

0.8

1.0

0 0.2

1.2

0.4

0.6

0.8

1.0

1.2

r(nm)

(b) 2.46% of pectin system 3

3

In the aqueous solution

At the liquid-solid interface

1ns 10ns 20ns

1ns 10ns 20ns

2

gC-C

2

gC-C

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

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1

1

0 0.2

0.4

0.6

0.8

r(nm)

1.0

1.2

0 0.2

0.4

0.6

0.8

1.0

1.2

r(nm)

(c) 3.62% of pectin system Fig 9. Radial distribution functions of carbon atoms of CH4 hydrate at different simulation time with pectin concentrations. (a) non-pectin system (b) 2.46% of pectin system (c) 3.62% of pectin system


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-26000

non-pectin system 2.46% of pectin in the aqueous solution 3.62% of pectin in the aqueous solution 2.46% of pectin at the liquid-solid interface 3.62% of pectin at the liquid-solid interface

-28000

Energy(KJ/mol)

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


-30000

-32000

0

5000

10000

15000

20000

Time(ps)

Fig 10. The variation of the total energy with time for different system.



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Table of Contents (TOC) Image


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Molecular Dynamics Simulation of Methane Hydrate Growth in the

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