Clathrates, more commonly known as gas hydrates, were discovered in 1810, yet they were considered a lab curiosity until recently.  Today, gas hydrates are studied both in labs and in situ.  Throughout these studies, the broad nature of the field has led to the development of two “camps” within the field, the physical chemistry and the environmental science.  These two camps are fundamentally different in their goals and interests.  Thus it is not surprising that these two camps have developed separate identities.  A significant benefit of this separation is each sect can pursue their own goals and interests leading to important scientific insights.  However, this barrier inhibits the development of a complete understanding of natural gas hydrates.
        In recent years, this barrier has become more obvious and more restrictive.  As hydrates have gained notoriety in the general scientific world as a key player in current issues such as global climate change and fuel resources, a large scale push has begun to understand hydrates inside and outside the laboratory.  This push requires the two camps to collaborate.
        One of the most interesting areas in which this collaboration can be seen is in the study of the structural properties of natural gas hydrates.  Clathrates (gas hydrates) are crystalline compounds consisting of an ice-like water lattice with a “guest” molecule trapped.  The water molecules form hydrogen bonds.  As pressure increases the water molecules are driven together eventually forming a polyhedron with a lattice hole.  (Figure 1)

        In this lattice hole, gases such as CO2, methane, ethane, propane, and higher molecular weight hydrocarbons are trapped, thereby forming hydrate.  Three distinctive structures have been identified, S-I, S-II, and S-H.  Of these S-I and S-II are well characterized, whereas S-H is a recent discovery, thus less understood.
        Each structure consists of at least two types of polyhedron structures.  The basic building block for all hydrates is the fundamental 512 polyhedron.  Slight modifications on this structure provide the foundation for the structure classifications in figure 2.  The geometry of the different structures is illustrated in table 1.

The geometry of the hydrate gives rise to strict rules as to the types of gases that each hydrate can “trap”.  The simplest image is to imagine trying to fit a ball into a cage; if the ball is too small the ball will fall out.  On the other hand, if the ball is too large the cage will break.  One method of determining theoretically whether a molecule will fit into a cavity is to calculate the molecular diameter to cavity diameter ratio.  If this ratio is under 1.00 then the gas hydrate structure should form.  For a complete analysis of standard natural gas components see table 2.  These estimates agree very well with experimental data collected through laboratory work.  Now these rules must be applied to natural hydrate deposits.

Table 1: Geometry of hydrate structures

	Structure I		Structure II		Structure H
	small	large	small	large	small	medium	large
Description	512	51262	512	51264	512	435663	51268
# Cavities	2	6	16	8	3	2	1
Cavity Radius	3.95	4.33	3.91	4.73	~ 3.91	~ 4.06	~ 5.71
Coorination #	20	24	20	28	20	20	36
# water	46		136		34

Table 2: molecular diameter/cavity diameter for major natural gas components

	diameter	512	51262	512	51264	512	435663	51268
N2	4.1	0.804	0.700	0.817	0.616	0.817	0.771	0.476
CH4	4.36	0.855	0.744	0.868	0.655	0.869	0.820	0.506
CO2	5.12	1.00	0.834	1.02	0.769	1.02	0.962	0.594
C2H6	5.5	1.08	0.939	1.10	0.826	1.10	1.03	0.638
C3H8	6.28	1.23	1.07	1.25	0.943	1.25	1.18	0.729
i-C4H10	6.5	1.27	1.11	1.29	0.976	1.29	1.22	0.754
n-C4H10	7.1	1.39	1.21	1.41	1.07	1.41	1.33	0.824

         Basic characterizations of the natural gas hydrate crystal structure have been performed.  It has been found that S-I and S-II hydrates exist in nature.  Most deep-sea deposits consist of primarily methane thus the preferred structure is S-I.  However, vents with more impurities tend to form S-II structures.² Only one in situ deposit of S-H hydrate has been observed from a thermogenic gas vent in the Gulf of Mexico.³ These tendencies provide a foundation for further studies into how hydrate structure effects the gas composition.
         Utilizing the unique technology available at Monterey Bay Aquarium Research Institute, two major hydrate deposits, Eel River Basin and Hydrate Ridge were studied. These studies included imaging, sampling, and observation of the sites.  In particular, gas samples were collected from gas vents and gas released from the sediment for gas chromatography analysis. These samples reveal a possible connection between hydrate formation and gas composition.
        The samples contain interesting results for both physical chemists and environmental scientists.   The samples from the Eel River sample site have high methane concentrations, and only slight concentrations of ethane and propane.  This composition is indicative of an S-I hydrate with a biogenic gas source.  There is little variation between the samples in hydrocarbon composition indicating that the samples stem from the same source.  The N2 + O2 and CO2 had some variation; however, this variation seems to vary in accordance with the distance the bubble travels in the water column prior to collection.  W11, W12, and W13 best illustrate this hypothesis.  These samples had increasing N2 + O2 concentration, while the CO2 concentrations decreased.  These changes represent the loss of CO2 to the water and the invasion of N2 + O2 into the bubble as the bubble rises through the water column.
        The Hydrate Ridge samples are very different from the familiar results seen at the Eel River site.  The Hydrate Ridge gas is believed to be a highly impure biogenic.  This was determined by evaluation of the C1/(C2+C3) ratio.  However, this cannot be confirmed without C13 data.  The samples contain two peculiar results.  First, the sample contained i-pentane and did not contain n-pentane; this is contrary to expected results.  It is expected that if i-pentane is present then so is n-pentane, since there is no known mechanism for their natural separation.  S-I and S-II hydrate cavities are too small to “trap” either pentane.  Thus, if the samples were decomposed gas from S-I or S-II hydrates no pentane would be observed.  S-H hydrate does “trap” i-pentane, but does not “trap” n-pentane.  Therefore a natural process for i-pentane and n-pentane separation could be the formation of S-H hydrates.  Another issue arises, in that, S-H hydrates have only been observed in nature once, in the Gulf of Mexico.3  This hydrate consisted of 41% I-pentane indicating a relatively pure S-H hydrate.  The Hydrate Ridge samples collected contained only trace amounts of i-pentane indicating that only a small percent of the sample is S-H hydrate, suggesting hydrate structure mixing.
             The second interesting aspect of the Hydrate Ridge samples is that they were super saturated with N2 + O2.  This saturation could reflect an error in the sampling practice or that hydrate formation could be a method of gas fractionation.  Possible sources of error are leaky cylinders or a faulty vacuum system; this is unlikely because the cylinders were filled with hydrogen, not air, to check for leaks prior to evacuation.  Therefore obtaining the air concentration requires air to be pumped into the system.  Conversely, the gas fractionation could have occurred due to formation of hydrate.  Hydrate structures vary in stability due to the composition and distribution of the gas molecules filling the cavity hole.  In the case of the Hydrate Ridge gas, which is high in methane concentration, the nitrogen and oxygen may have been selectively excluded in favor of the more stabilizing methane.  Thus a theoritical study was designed to compare the repective stablities of the hydrate structure fill with differing gases.

METHOD:

In order to perform energy calculation the a structure 1 hydrate file had to be perpared for Hyper-Chem. Preparing this file encompased much of the semester, and was a complcated process.

1) X-Ray Crystalograpy data was found for a structure I hydrate molecule.
 Literature source:

2) This data was inputed into NRCVAX with slight modifications to account for the variable guest molecule. The data which is inputted is the space group, cordinates given by X-Ray crystalography file, occupany, and multiplicaty. This data can be viewed in ORTEP or PLUTO. The using the UTLITY program a coordinate printout can be obtained for a full cell of the structure built.

3) The file outputed from the Utlity program can be easily modified into an *.xyz file
Example:

236 =  # of atoms

name       x             y            z
O1a    2.20895  2.20895  2.20895
O1b    9.82105  9.82105  9.82105
O1c    2.20895  2.20895  9.82105
O1d    9.82105  9.82105  2.20895
O1e    2.20895  9.82105  9.82105
O1f     9.82105  2.20895  2.20895
O1g    9.82105  2.20895  9.82105
O1h    2.20895  9.82105  2.20895
O1i     8.22395  8.22395  8.22395
O1j     3.80605  3.80605  3.80605
O1k    8.22395  8.22395  3.80605
O1l     3.80605  3.80605  8.22395
O1m   3.80605  8.22395  3.80605
O1n    8.22395  3.80605  8.22395
O1o    8.22395  3.80605  3.80605
O1p    3.80605  8.22395  8.22395

This file can then be opened in gOpenMol to edit bonds ect. and a picture can be obtained.

4) This file can be saved as a *.pbd and imported into Hyper-Chem for finalization.
5) Once finalized the HyperChem file should be saved as an *.ent and then manually converted into a *.xtl file

246 = # of atoms 1.0 1.0 1.0 = cell unit in x,y,z 1.00 1.25= bond distances Methane Hydrate = name
12.5 12.5 12.5= cell edge  90.0 90.0 90.0 =cell angles   S.G.=space group
     x            y           z        at. #    name
 0.17928 0.18480  0.19192    8        O1
 0.23208 0.23616  0.24192    1        H2
 0.09872 0.22328  0.17320    1        H3
 0.50000 0.00000  0.25000    6        C4
 0.55240 0.05232  0.30240    1        H5
 0.44760 0.05232  0.30240    1        H6
 0.55240 0.05232  0.19760    1        H7
 0.44760 0.05232  0.19760    1        H8
 0.50000 1.00000  0.25000    6        C9
 0.44760 0.94760  0.30240    1        H10
 0.55232 0.94760  0.30240    1        H11
 0.44760 0.94760  0.19760    1        H12
 0.55232 0.94760  0.19760    1        H13
distance in fractional coordinates

This *.xtl was then imported into a program in development called xtlw0.1. This program will take the sigle unit cell given in the *.xtl file and expand it into a large segment of the structure. I expanded my crystal structure until I got two full lattices and multiple half lattices. This program opens directly into HyperChem.

6) At this point I hand-pruned the hydrogen molecules to two pre oxygen. This was necessary becuase the is no way to account for the half hydrogens in HyperChem. After many hours of work I obtained the following structure

7) Using this previous structure as a base calculations were run to determine the various energies for various hydrate structure to determine relative stablities.
 
 

Energies:

scf-atom-energy gives isolated atom energy from semi-emperical method
scf-core-energy gives core-core interaction energy
scf-electronic-energy gives the electronic energy for a semi-emperical calculation
scf-binding-energy gives energy relative to isolated atoms

 

As expected intial calculation indicate that the CH4 does significantly better at stablizing the lattice stucture, -11374 kcal/mol opposed to -5057 kcal/mol. The N2 stablizion is only slightly better than that of a cell with a hole and gas outside. The data also indicates that in the presence of Gas the hydrate lattice is better stablized with the gas molecule trapped inside not outside.Also, this project has shown that hydrate can be modeled using HyperChem and meaningful energies can be calculated.
 

1 Sloan, E.D.(1998). Gas Hydrates: Review of Physical/Chemical Properties. Energy & Fuels, 12: 191-196.

2 Kvenvolden, K.A. (1996). Methane Hydrate- a major reservoir of carbon in the shallow geosphere? Chemical Geology, 71: 41-51.

3 Sasson, R. and I.R. MacDonald (1994). Evidence of structure H hydrate, Gulf of Mexico continental slope. Organic Geochemistry, 22: 1029-1032.
 

References:

Brewer, P.G.; F.M. Orr; G. Friederich; K.A.  and D.L. Orange (1998). Gas Hydrate Formation in the Deep Sea: In Situ Experiments with Controlled Release of Methane, Natural Gas, and Carbon Dioxide. Energy & Fuels, 12: 183-188.

Brooks, J.M.; M.E. Field and M.C. Kennicutt (1991). Observations of gas hydrates in marine sediment, offshore northern California. Marine Geology, 96: 103-109.

Kvenvolden, K.A. (1988). A primer on the geological occurrence of Gas Hydrate. First MASTER Workshop Tutorial Book, p.39-80.

Kvenvolden, K.A. (2000). Gas Hydrate and Humans. Annals of the New York Academy of Science, 912:17-22.

Mehta A.P. and E.D. Sloan (1994). A thermodynamic Model for Structure-H Hydrates. AIChE Journal, 40: 312-320.

Peltzer, E.T. and P.G. Brewer (in press) Practical Physical Chemistry and Empirical Predictions of Methane Hydrate Stability.

Ripmeester, J.A. (2000). Hydrate Research—From Correlation to a Knowledge-based Discipline. Annals of the New York Academy of Science, 912: 1-16.

Sasson, R. and I.R. MacDonald (1997). Hydrocarbons of experimental and natural gas hydrates, Gulf of Mexico continental slope. Organic Geochemistry, 26: 289-293.

Sloan, E.D., Clathrate hydrates of natural gases. Marcel Dekker, NY, 641 pp. (1990).

Sloan, E.D.(1996). Physical and Chemical Properties of Gas Hydrates and Applications to World Margin Stability and Climatic Change. First MASTER Workshop Tutorial Book, p.1-38.

Zapsepina, O. Ye. and B.A. Buffet (1997). Phase equilibrium of gas hydrate: Implications for the formation of hydrate on the deep sea floor. Geophysical  Research Letters, 24: 1567-1570.