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Journal of Chemistry

Volume 2013 (2013), Article ID 415027, 10 pages

http://dx.doi.org/10.1155/2013/415027

## Molecular Dynamics Simulations of CO_{2} Molecules in ZIF-11 Using Refined AMBER Force Field

^{1}The Applied Mathematics Research Group (AMRG), Department of Mathematics, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand^{2}Faculty of Applied Science and Engineering, Nong Khai Campus, Khon Kaen University, Nong Khai 43000, Thailand

Received 1 August 2013; Accepted 8 September 2013

Academic Editor: Hakan Arslan

Copyright © 2013 W. Wongsinlatam and T. Remsungnen. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

#### Abstract

Nonbonding parameters of AMBER force field have been refined based on *ab initio* binding energies of CO_{2}–[C_{7}H_{5}N_{2}]^{−} complexes. The energy and geometry scaling factors are obtained to be 1.2 and 0.9 for and parameters, respectively. Molecular dynamics simulations of CO_{2} molecules in rigid framework ZIF-11, have then been performed using original AMBER parameters (SIM I) and refined parameters (SIM II), respectively. The site-site radial distribution functions and the molecular distribution plots simulations indicate that all hydrogen atoms are favored binding site of CO_{2} molecules. One slight but notable difference is that CO_{2} molecules are mostly located around and closer to hydrogen atom of imidazolate ring in SIM II than those found in SIM I. The Zn-Zn and Zn-N RDFs in free flexible framework simulation (SIM III) show validity of adapting AMBER bonding parameters. Due to the limitations of computing resources and times in this study, the results of flexible framework simulation using refined nonbonding AMBER parameters (SIM IV) are not much different from those obtained in SIM II.

#### 1. Introduction

The increase in carbon dioxide (CO_{2}) in Earth’s atmosphere is a subject of worldwide attention as being the cause of global warming. Human activities such as combustion of fossil fuels (coal, oil, and natural gas) in power plants, automobiles, and industrial facilities are main sources of CO_{2} emission. The cost-effective and scalable technologies to capture and store CO_{2} are now of great interest [1–7]. The low energy requirement technologies based on adsorption processes are highlighted as promising methods, stimulating recent works to investigate suitable adsorbent materials. Metal-organic frameworks (MOFs) are a class of nanoporous materials that are promising candidates for CO_{2} capture, due to their potential applications in separation processes, catalysis, and gas storage [8–14]. Zeolitic imidazolate frameworks (ZIFs) are subclass of MOFs, in which positive metal ions such as Zn, Co, and Cu are linked by ditopic imidazolate ligands [15, 16]. Some ZIFs are attracted as materials which are used to keep the emissions of CO_{2} out of the atmosphere in hot energy-producing environments like power plants due to their exceptional chemical and thermal stabilities and nontoxic crystals [17–19]. The ZIF-11 is one of ZIFs which exhibits the RHO topology. It is composed of Zn^{2+} ion clusters linked by dipotic benzimidazolate ([C_{7}H_{5}N_{2}]^{−}) ligands with chemical formula Zn[C_{7}H_{5}N_{2}]_{2} [15] (see Figure 1).

The high-throughput methods can be successfully applied to the development a robust synthesis protocol for several ZIFs in short time [20]. Computer models and simulations can be used to rapidly screen and develop promising ZIFs with large savings in experimental time and cost [9]. There are some computer simulations where bonding and non-bonding parameters of general force fields such as AMBER are applied [21]. This is one of well-known force fields that supplies reliable intramolecular force constants within the organic linker; however it is not developed directly for the system of MOFs or ZIFs as in this study.

In this study, the protocol to refine and validate molecular interactions was obtained from general force fields in order to meet both accuracy and time saving for using in specific system like adsorption of CO_{2} in ZIF-11. Since some investigations show that the imidazolate organic linker is most favored adsorption site of guest molecules [17–19], by assumption the interactions between CO_{2} and ZIF-11 frameworks are almost contributed by interactions between CO_{2} molecule and [C_{7}H_{5}N_{2}]^{−} groups. Nonbonding parameters obtained from AMBER force field are refined using *ab initio* data corresponding to the calculated partial atomic charge. The bonding parameters of AMBER force field are also adapted to represent the flexible framework of ZIF-11. Molecular dynamics simulations of rigid and flexible frameworks are done in order to validate the parameters.

#### 2. Material and Methods

##### 2.1. Models of CO_{2} and ZIF-11 Framework

In this study, a geometrical structure of [C_{7}H_{5}N_{2}]^{−} is cut directly from ZIF-11 framework [15] and is not theoretical optimized (see Figure 1). The linear rigid model of CO_{2} molecule is taken from [22] with C–O bond length of 1.16 Å and O–C–O bond angle of 180°. The partial atomic charges of [C_{7}H_{5}N_{2}]^{−} were computed according to the Merz-Singh-Kollman scheme [23, 24] and then further refined these ESP charges to so-called RESP charges using an Antechamber package [21, 25] with a total charge of −1, while the partial charge of the Zn^{2+} was fixed to be +2. The force fields and simulations atom types and their corresponding atomic partial charges are shown in Table 1.

##### 2.2. Single Point Energies of CO_{2}–[C_{7}H_{5}N_{2}]^{−} Complexes

The binding energy, , of a CO_{2}–[C_{7}H_{5}N_{2}]^{−} complex is defined on the basis of the supermolecular approach according to
where , , and are the total energy of complex, the energy of CO_{2} molecule, and the energy of [C_{7}H_{5}N_{2}]^{−}, respectively. The binding energy without basis set superposition error (BSSE) correction of a complex is defined as
where denotes the total energy of the complex AB calculated with the full basis set of the complex. The and denote the total energies of the monomers and , each calculated with its basis sets, respectively. The counterpoise BSSE corrected binding energy [26] is represented by
where , , and denote the total energy of complex, the energy of monomer , and the energy of monomer which are computed using the union of the two basis sets of monomer and , respectively.

Several structures of CO_{2}–[C_{7}H_{5}N_{2}]^{−} complexes are generated by varying positions and orientations of CO_{2} molecule around [C_{7}H_{5}N_{2}]^{−} (see Figure 2). Then their corresponding binding energies without and with BSSE correction were calculated at level of HF/6-31G* using Gaussian 09 package [27]. These energies are used as data for refinement nonbonding parameters of AMBER force field.

##### 2.3. The Parameters of the Intramolecular and Intermolecular Interactions

In this study, the functions in the AMBER force field which is known to be reliable for biomolecules and organic species are adopted to represent CO_{2} molecules in ZIF-11 framework system as follows:
The intramolecular energy, , includes bond stretching and bending and proper and improper torsional potentials:
The parameters used to describe the flexibility of ZIF-8 framework from previous studies [28–30] are adopted for ZIF-11 framework in this study and are summarized in Table 2.

The AMBER force field describes the nonbonding interaction of two atom sites, and with Lennard-Jones parameters and the following formula

The Lorentz-Berthelot mixing rules were applied to obtain the cross-interactions parameters and (see Table 3) between different atom types, and [31–33], with and . Formula (6) can be transformed into where and , respectively.

##### 2.4. Molecular Dynamics Simulations of CO_{2} Molecules in ZIF-11

All MD simulations are performed using DL_POLY (version 2.20) package [34] in canonical ensemble (NVT) for 9 CO_{2} molecules in the ZIF-11 frameworks (see Figure 3).

The simulations box with a cubic length of 57.52 Å, subject to periodic boundary conditions, consists of unit cells of ZIF-11, which contains at least 9 full cages (see Figure 3). This corresponds to a loading of about one CO_{2} molecule per unit cell. The precision of Ewald summation for long length dispersion force had been set to 0.0001. In order to maintain a constant temperature of 300 K, the Nosé-Hoover thermostat with a relaxation time and time step of 0.001 ps was applied along the whole simulations. The simulations were equilibrated for 1,000,000 time steps (1 ns), and then further simulations of 1 ns were carried out in order to provide data for structural and dynamical properties evaluation. There are four simulations in this study and denote as SIM I, SIM II, SIM III, and SIM IV for the rigid framework simulations using original AMBER force field, the rigid framework simulations using sAMBER force field, the flexible framework simulations for free ZIF-11, and the flexible framework simulations for CO_{2} in the ZIF-11 using sAMBER force field, respectively.

#### 3. Results and Discussion

##### 3.1. Obtained Refined Parameters

By using the BSSE corrected *ab initio* binding energies as data to refine the AMBER parameters, the energy and geometry scaling factors are obtained to be 1.2 and 0.9 for and , respectively. The consequence and parameters for original and scaled parameters are summarized in Table 4 while Figure 4 shows the comparison between , , and energies of CO_{2}–[C_{7}H_{5}N_{2}]^{−} complexes. The results show that all and parameters of scaled AMBER are less than those obtained from original AMBER but the total binding energy is more close to the *ab initio* data. Then only the sAMBER parameters are used in the flexible framework simulation.

##### 3.2. Molecular Dynamics Simulations of CO_{2} Molecules in Rigid ZIF-11 Framework

The radial distribution functions (RDFs) are used to measure the distribution of intermolecular distances between CO_{2} molecules and the framework of ZIF-11. All RDFs for rigid simulations (see Figures 5 and 6) show notable difference between both simulations, that is, in SIM II, the CO_{2} molecules lie closer to the [C_{7}H_{5}N_{2}]^{−} groups than those obtained from SIM I. The smallest distance is found of about 2.5 Å with a first peak of about 3.0 Å in H1-O RDF (see Figure 5(d)) of SIM II, while these distances are increased by about 0.9 Å in H1-O RDF of SIM I. This makes sense, since the energies and the geometrical parameters of sAMBER are stronger and shorter than those of original AMBER. The favorite adsorption sites of CO_{2} molecules are found at H3 and H4 positions in SIM I, while all hydrogen atoms (H1, H3, and H4) are equally favored in SIM II. One can say that CO_{2} molecules are found more located around H1 in SIM II than those found in SIM I. The distribution plots in Figure 7 indicate that in both simulations, all CO_{2} molecules are located only in one pore along the whole simulation times. In addition, CO_{2} molecules in SIM II obtained a bit wider distribution than those in SIM I. The self-diffusion coefficients of CO_{2} molecules are obtained as m^{2}/s and m^{2}/s in SIM I and SIM II, respectively, being less than those obtained in ZIF-8 [18, 35], ZIF-68, and ZIF-69 [19].

##### 3.3. Molecular Dynamics Simulations of CO_{2} Molecules in Flexible ZIF-11 Framework

The flexibility of the framework is modeled by AMBER force field with the RESP partial atomic charges. The free framework simulation (SIM III) had been done first. The RDFs of Zn-Zn and Zn-N of ZIF-11 frameworks (see Figure 8) are plotted in comparison to those obtained from XRD data (SIM I). The results show that the flexible model can remain the main structure of the frameworks without collapsing during the whole simulations. This indicates the validity of the flexible model at least for NVT ensembles that used in this study. Moreover the CO_{2}-framework interactions models in SIM IV simulation have no significant effect on the main flexible structure of the framework.

The RDFs of ZIF-11 framework and CO_{2} molecules are shown in Figures 9 and 10. The oriented structure of CO_{2} molecules in ZIF-11 obtained from flexible framework simulation is similar to those obtained from rigid framework simulations (SIM II). Slight difference can be obtained in the distribution plot (see Figure 7) which indicates that H1 is more favorable binding site than H3 and H4. The distributed areas which obtained from the flexible simulation (Figure 7(c)) are smaller than those obtained from the rigid simulations (Figures 7(a) and 7(b)). This corresponding to almost zero value (less than 10^{−14} m^{2}/s) of obtained self-diffusion coefficient of CO_{2} in flexible framework. It is difficult to point here that this value is realizable or not. However some previous work [18] convinces that ZIF-11 framework is promising to use for separate CO_{2} from natural gases.

#### 4. Conclusion

Several single point interaction energies of CO_{2}–[C_{7}H_{5}N_{2}]^{−} complexes are calculated and this data was used in the processes of modifying the general AMBER force field. The method of calculations at HF/6-31G* gives large BSSE which needs to be corrected in order to have accurate binding energies. The rigid framework simulations, SIM I and SIM II, give similar results; that is, all hydrogen sites are favored binding site but CO_{2} molecules are found more located around H1 in SIM II than those found in SIM I. Due to the limited time and computer resources, we success only a flexible simulations for testing parameters both intramolecular and intermolecular interactions. However the results which obtained from flexible simulations are not much different from those obtained from rigid framework simulations. The distribution plots are slightly different which indicates that H1 is more favorable binding site than H3 and H4. Until now this study is one of the successful works on flexible ZIF-11.

In further works, one should focus to try some other both rigid and flexible models of CO_{2} molecules and also other flexible force fileds of ZIF-11. Several simulations such as varying number of CO_{2} molecules in the framework and mixing CO_{2} molecules with other natural gases molecules are of great interest.

#### Conflict of Interests

The authors declare that there is no conflict of interests regarding the publication of this paper.

#### Acknowledgments

The authors would like to thank the Higher Education Research Promotion and National Research University Project of Thailand, Office of Higher Education Commission, through the Advanced Functional Materials Cluster of Khon Kaen University.

#### References

- G. I. Panov, A. K. Uriarte, M. A. Rodkin, and V. I. Sobolev, “Generation of active oxygen species on solid surfaces. Opportunity for novel oxidation technologies over zeolites,”
*Catalysis Today*, vol. 41, no. 4, pp. 365–385, 1998. View at Google Scholar · View at Scopus - J. A. Z. Pieterse, G. Mul, I. Melian-Cabrera, and R. W. van den Brink, “Synergy between metals in bimetallic zeolite supported catalyst for NO-promoted N
_{2}O decomposition,”*Catalysis Letters*, vol. 99, no. 1-2, pp. 41–44, 2005. View at Publisher · View at Google Scholar · View at Scopus - W. F. Hoelderich, “Environmentally benign manufacturing of fine and intermediate chemicals,”
*Catalysis Today*, vol. 62, no. 1, pp. 115–130, 2000. View at Publisher · View at Google Scholar · View at Scopus - Q. M. Wang, D. Shen, M. Bülow et al., “Metallo-organic molecular sieve for gas separation and purification,”
*Microporous and Mesoporous Materials*, vol. 55, no. 2, pp. 217–230, 2002. View at Google Scholar · View at Scopus - H. Rodhe, “A comparison of the contribution of various gases to the greenhouse effect,”
*Science*, vol. 248, no. 4960, pp. 1217–1219, 1990. View at Google Scholar · View at Scopus - G. Centi, S. Perathoner, and F. Vazzana, “Catalytic control of non-CO
_{2}greenhouse gases: methane, fluorocarbons, and especially nitrous oxide can be decomposed and even reused by implementing new catalytic techniques,”*ChemTech*, vol. 29, no. 12, pp. 48–55, 1999. View at Google Scholar · View at Scopus - H. K. Song, K. W. Cho, and K. H. Lee, “Adsorption of carbon dioxide on the chemically modified silica adsorbents,”
*Journal of Non-Crystalline Solids*, vol. 242, no. 2-3, pp. 69–80, 1998. View at Google Scholar · View at Scopus - J. R. Li, Y. Ma, M. C. McCarthy et al., “Carbon dioxide capture-related gas adsorption and separation in metal-organic frameworks,”
*Coordination Chemistry Reviews*, vol. 255, no. 15-16, pp. 1791–1823, 2011. View at Publisher · View at Google Scholar · View at Scopus - A. O. Yazaydin, R. Q. Snurr, T. Park et al., “Screening of metal-organic frameworks for carbon dioxide capture from flue gas using a combined experimental and modeling approach,”
*Journal of the American Chemical Society*, vol. 131, no. 51, pp. 18198–18199, 2009. View at Publisher · View at Google Scholar · View at Scopus - D. Saha, Z. Bao, F. Jia, and S. Deng, “Adsorption of CO
_{2}, CH_{4}, N_{2}O, and N_{2}on MOF-5, MOF-177, and zeolite 5A,”*Environmental Science and Technology*, vol. 44, no. 5, pp. 1820–1826, 2010. View at Publisher · View at Google Scholar · View at Scopus - C. M. Lu, J. Liu, K. Xiao, and A. T. Harris, “Microwave enhanced synthesis of MOF-5 and its CO
_{2}capture ability at moderate temperatures across multiple capture and release cycles,”*Chemical Engineering Journal*, vol. 156, no. 2, pp. 465–470, 2010. View at Publisher · View at Google Scholar · View at Scopus - Q. Yang, C. Zhong, and J. F. Chen, “Computational study of CO
_{2}storage in metal-organic frameworks,”*Journal of Physical Chemistry C*, vol. 112, no. 5, pp. 1562–1569, 2008. View at Publisher · View at Google Scholar · View at Scopus - A. G. Wong-Foy, A. J. Matzger, and O. M. Yaghi, “Exceptional H
_{2}saturation uptake in microporous metal-organic frameworks,”*Journal of the American Chemical Society*, vol. 128, no. 11, pp. 3494–3495, 2006. View at Publisher · View at Google Scholar · View at Scopus - Y. Li and R. T. Yang, “Gas adsorption and storage in metal-organic framework MOF-177,”
*Langmuir*, vol. 23, no. 26, pp. 12937–12944, 2007. View at Publisher · View at Google Scholar · View at Scopus - K. S. Park, Z. Ni, A. P. Côté et al., “Exceptional chemical and thermal stability of zeolitic imidazolate frameworks,”
*Proceedings of the National Academy of Sciences of the United States of America*, vol. 103, no. 27, pp. 10186–10191, 2006. View at Publisher · View at Google Scholar · View at Scopus - J. C. Tan, T. D. Bennett, and A. K. Cheetham, “Chemical structure, network topology, and porosity effects on the mechanical properties of zeolitic imidazolate frameworks,”
*Proceedings of the National Academy of Sciences of the United States of America*, vol. 107, no. 22, pp. 9938–9943, 2010. View at Publisher · View at Google Scholar · View at Scopus - B. Wang, A. P. Côté, H. Furukawa, M. O'Keeffe, and O. M. Yaghi, “Colossal cages in zeolitic imidazolate frameworks as selective carbon dioxide reservoirs,”
*Nature*, vol. 453, no. 7192, pp. 207–211, 2008. View at Publisher · View at Google Scholar · View at Scopus - M. William, H. Ning, G. Keith et al., “A combined experimental-computational study on the effect of topology on carbon dioxide adsorption in zeolitic imidazolate frameworks,”
*Journal of Physical Chemistry C*, vol. 116, no. 45, pp. 24084–24090, 2012. View at Publisher · View at Google Scholar - D. Liu, C. Zheng, Q. Yang, and C. Zhong, “Understanding the adsorption and diffusion of carbon dioxide in zeolitic imidazolate frameworks: a molecular simulation study,”
*Journal of Physical Chemistry C*, vol. 113, no. 12, pp. 5004–5009, 2009. View at Publisher · View at Google Scholar · View at Scopus - R. Banerjee, A. Phan, B. Wang et al., “High-throughput synthesis of zeolitic imidazolate frameworks and application to CO
_{2}capture,”*Science*, vol. 319, no. 5865, pp. 939–943, 2008. View at Publisher · View at Google Scholar · View at Scopus - J. M. Wang, R. M. Wolf, J. W. Caldwell, P. A. Kollman, and D. A. Case, “Development and testing of a general amber force field,”
*Journal of Computational Chemistry*, vol. 25, no. 9, pp. 1157–1174, 2004. View at Publisher · View at Google Scholar · View at Scopus - C. S. Murthy, K. Singer, and I. R. Mcdonald, “Interaction site models for carbon dioxide,”
*Molecular Physics*, vol. 44, no. 1, pp. 135–143, 1981. View at Publisher · View at Google Scholar - U. C. Singh and P. A. Kollman, “An approach to computing electrostatic charges for molecules,”
*Journal of Computational Chemistry*, vol. 5, no. 2, pp. 129–145, 1984. View at Publisher · View at Google Scholar - B. H. Besler, K. M. Merz Jr., and P. A. Kollman, “Atomic charges derived from semiempirical methods,”
*Journal of Computational Chemistry*, vol. 11, no. 4, pp. 431–439, 1990. View at Publisher · View at Google Scholar - J. Wang, W. Wang, P. A. Kollman, and D. A. Case, “Automatic atom type and bond type perception in molecular mechanical calculations,”
*Journal of Molecular Graphics and Modelling*, vol. 25, no. 2, pp. 247–260, 2006. View at Publisher · View at Google Scholar · View at Scopus - S. F. Boys and F. Bernardi, “The calculation of small molecular interactions by the differences of separate total energies,”
*Molecular Physics*, vol. 19, no. 4, pp. 553–566, 1970. View at Publisher · View at Google Scholar - M. J. Frisch, H. B. Schlegel, G. E. Scuseria et al.,
*Gaussian 09 Revision A1*, Gaussian Inc., Wallingford, Conn, USA, 2009. - L. Hertäg, H. Bux, J. Caro et al., “Diffusion of CH
_{4}and H_{2}in ZIF-8,”*Journal of Membrane Science*, vol. 377, no. 1-2, pp. 36–41, 2011. View at Publisher · View at Google Scholar · View at Scopus - H. Zhongqiao, Z. Liling, and J. Jianwen, “Development of a force field for zeolitic imidazolate framework-8 with structural flexibility,”
*Journal of Chemical Physics*, vol. 136, no. 3, pp. 244–703, 2012. View at Google Scholar - B. Zheng, M. Sant, P. Demontis, and G. B. Suffritti, “Force field for molecular dynamics computations in flexible ZIF-8 framework,”
*Journal of Physical Chemistry C*, vol. 116, no. 1, pp. 933–938, 2012. View at Publisher · View at Google Scholar · View at Scopus - H. A. Lorentz, “Ueber die Anwendung des Satzes vom Virial in der kinetischen Theorie der Gase,”
*Annalen der Physik*, vol. 248, no. 1, pp. 127–136, 1881. View at Google Scholar - D. Berthelot, “Sur le mélange des gaz,”
*Comptes Rendus Hebdomadaires des Séances de l'Académie des Sciences*, vol. 126, pp. 1703–1855, 1898. View at Google Scholar - J. Delhommelle and P. Millié, “Inadequacy of the Lorentz-Berthelot combining rules for accurate predictions of equilibrium properties by molecular simulation,”
*Molecular Physics*, vol. 99, no. 8, pp. 619–625, 2001. View at Publisher · View at Google Scholar · View at Scopus - W. Smith and T. R. Forester, “DL-POLY-2.0: a general-purpose parallel molecular dynamics simulation package,”
*Journal of Molecular Graphics*, vol. 14, no. 3, pp. 136–141, 1996. View at Publisher · View at Google Scholar · View at Scopus - P. Puphasuk and T. Remsungnen, “Structures and dynamics of CO
_{2}molecules in zeolitic imidazolate frameworks-8: molecular dynamics simulations using*ab initio*fitted interaction and generic force fields,”*Journal of Computational and Theoretical Nanoscience*, vol. 10, no. 1, pp. 227–231, 2013. View at Publisher · View at Google Scholar