Supplementary Information. Theoretical Optimization of Pore Size and. Chemistry in SIFSIX-3-M Hybrid. Ultramicroporous Materials

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1 Supplementary Information Theoretical Optimization of Pore Size and Chemistry in SIFSIX-3-M Hybrid Ultramicroporous Materials Ahmad Ziaee 1,2, Drahomir Chovan 1,2, John J. Perry IV 2,3, Michael J. Zaworotko 2,3,* and Syed A.M. Tofail 1,2,* 1 Department of Physics and Energy, University of Limerick, Republic of Ireland 2 Materials and Surface Science Institute, University of Limerick, Republic of Ireland 3 Bernal Institute; Department of Chemical and Environmental Science, University of Limerick, Republic of Ireland Authors to whom correspondence should be addressed: Michael.Zaworotko@ul.ie; Tofail.Syed@ul.ie 1

2 Table of Contents Materials... 3 Density Functional Theory (DFT)... 4 Molecular Mechanics Using GCMC and MD... 7 Partial Electrostatic Charges Calculation... 7 Adsorption Isotherms Adsorption Sites of CO 2 within SIFSIX-3-Cu and SIFSIX-3-Ni HUMs References

3 Materials For this study, three isostructural HUM compounds from the SIFSIX family 1 were investigated. The crystal structures of SIFSIX-3-Zn 1e (reference code FUDQIF) and SIFSIX-3-Cu 1d (reference code WONKOB) were obtained from the Cambridge Structural Database (CSD). 2 The crystal structure of SIFSIX-3-Ni was recently reported in two publications. 3 The crystallographic data is presented in Figure S1. A cell of SIFSIX-3-Zn (a) side view (b) top view. Atom colors: F = cyan, Zn = purple, Si = yellow, H = white, C = gray, N = blue. S1 and Table S2. Table S1. Unit cell parameters and pore size of the HUMs compounds. HUM a (Å) b (Å) c (Å) Pore Size (Å) SIFSIX-3-Zn (10) (10) (15) 3.84 SIFSIX-3-Ni (2) (2) (2) 3.55 SIFSIX-3-Cu (2) (2) (3) 3.42 Table S2. Experimental and simulated bond lengths and unit cell dimensions. Bond SIFSIX-3-Zn 4 SIFSIX-3-Ni 3a SIFSIX-3-Cu 1d Experimental (Å) Simulated (Å) Experimental (Å) Simulated (Å) Experimental (Å) Simulated (Å) Si-F equ Si-F axial M-F axial M-N N-C C-C C-H Unit Cell Dimensions 3

4 a = b c A supercell of the SIFSIX-3-Zn compound can be seen in Figure S1. Note that SIFSIX-3-Cu and SIFSIX-3-Ni are isostructural compounds with SIFSIX-3-Zn, but with slightly different unit cell dimensions. The unit cell parameters and pore-size (i.e. the distance across the channel as measured between diagonal metal nodes in ab-plane, minus van der Waals radii) of the three studied HUMs are also presented in Table S1. All the HUMs studied here crystallize in the tetragonal crystal system with P4/mmm space group. SIFSIX-3-Cu has the smallest pore-size followed by SIFSIX-3-Ni and SIFSIX-3-Zn, respectively. (a) (b) Figure S1. A cell of SIFSIX-3-Zn (a) side view (b) top view. Atom colors: F = cyan, Zn = purple, Si = yellow, H = white, C = gray, N = blue. Density Functional Theory (DFT) 4

5 In order to address the uncertainty about the position of equatorial fluorine atoms in the SIFSIX-3-M compounds, the structure was optimized followed by single-point energy calculations comparing various equatorial fluorine atom configurations. The optimization process was done in two steps: first, the unit cell dimensions were constrained while the atomic positions were optimized. Second, the unit cell parameters were allowed to relax. A plane-wave basis set and projector augmented wave (PAW) 5 technique was employed using Quantum ESPRESSO. 6 The Perdew, Burke and Ernzerhof (PBE) 7 parameterized generalized gradient approximation (GGA) functional was used for describing exchange and correlation. Ultrasoft Vanderbilt pseudopotentials 8 were used for all atoms, treating 3d 9 4s 1 orbitals for nickel, 3d 10 4s 1 orbitals for copper, and 3d 10 4s 2 orbitals for zinc as valence states. A kinetic energy cut-off of 550 ev was used and kept constant during all calculations. Also, Brillouinzone sampling was performed using an Monkhorst-Pack mesh scheme. 9 The optimization process was considered converged when the difference in energy of electron density was less than 10-6 ev and the forces acting on ions were less than 10-4 ev Å -1. Grimme s dispersion correction 10 was used to overcome the intrinsic lack of long-range electron correlation, which are responsible for van der Waals interactions 11 in DFT calculations. Following structure optimization, single-point energies were calculated for empty HUM pores, where equatorial fluorine atoms were deviated from their initial configuration at 5 intervals with respect to the a-axis. This process confirms the optimum configuration of fluorine atoms in empty pores is 45. However, this does not guarantee that the same configuration is adopted in a CO 2 loaded pore. In order to determine the equatorial fluorine configuration in loaded pores, the interaction energy between one CO 2 molecule and the HUM structure (delta E) was calculated by using equation 1 and these results were compared to experimental Q st values. 5

6 (1) Where, is the energy of the pore when loaded with CO 2 molecule, and are the energies of the CO 2 molecule and HUM pore. For this purpose, one CO 2 molecule was located at its optimized adsorption position (Figure S2) within the pore while the angle of fluorine atoms was varied at 5 intervals with respect to the a-axis. In a second step, the interaction energy was again calculated, but this time the fluorine configuration was held fixed at the previously determined 45 while the CO 2 position was varied by moving it vertically within the SIFSIX-3-M pore (i.e. parallel with the c-axis) using intervals of 0.1 Å. (a) (b) 6 (c) Figure S2. Depiction of a single CO 2 molecule within the pore structure of SIFSIX-3-M. (a) SIFSIX-3-Zn (b) SIFSIX-3-Ni (c) SIFSIX-3-Cu. Atom colors: F = cyan, Cu = red, Si = yellow, H = white, C = grey, N = blue, Ni = green, Zn = purple.

7 Molecular Mechanics Using GCMC and MD Total potential energy function for the sorbate-sorbent system during GCMC and MD calculations are based on the following components: + + (2) where, U vdw is the van der Waals potential energy, U el is the electrostatic potential energy and U intra is the intramolecular energy of the sorbate molecules. The intramolecular energy of the sorbent structure is disregarded since the HUM structure is assumed to be rigid during the GCMC simulation steps. Van der Waals repulsion/dispersion potential energy is based on 12-6 Lennard-Jones potential 12 equation: 4 (3) 7

8 where, ε ij is potential well depth between atoms i and j, σ ij is the zero potential distance between atoms i and j, and r ij is the distance between atoms i and j. Lorentz-Berthelot mixing rule was used for defining interatomic Lennard-Jones potential parameters of dissimilar atoms. 13 Electrostatic potential contribution to the total potential energy is obtained based on Coulomb equation: (4) where, q i and q j are partial charges of atoms i and j and r ij is the distance between two atoms. In this study the electrostatic interactions were calculated using Ewald summation method 14 with the accuracy of 10-4 kcal mol -1. Partial Electrostatic Charges Calculation The electrostatic potential surface of the HUMs was calculated by NWChem ab initio simulation package. 15 CHELPG scheme 16 were used to fit partial charges to the atomic centers to replicate the electrostatic potential surface. Crystallography reveals that, in regard to their partial charges, seven chemically distinct atoms can be specified in each SIFSIX-3-M HUM (Figure S3). For this purpose, the HUMs supercells have been truncated (sliced) along various directions (Figure S4; Fragments 1-14). Partial charges were determined for all atoms in the fragments, disregarding any buried or terminal atoms. The average partial electrostatic charges were fitted to the atomic centers. The electrostatic potential energy surface for these fragments was calculated by using 6-31G * basis set 17 for all atoms, except the metal nodes. The semi-relativistic pseudopotential LANL2DZ 18 was used for the many electron metal nodes of Zn 2+, Ni 2+ and Cu 2+. Average electrostatic charges used in GCMC calculations are shown in Table S6. The electrostatic charges of SIFSIX-3-Zn were derived previously. 19 8

9 Figure S3. Chemically distinct atoms in SIFSIX-3-Zn. Atom colors: F = cyan, Zn = purple, Si = yellow, H = white, C = gray, N = blue. 9

10 Table S3. Partial electrostatic charges on different fragments of SIFSIX-3-Zn. Atom Label Frag 1 Frag 2 Frag 3 Frag 4 Frag 5 Frag 6 Frag 7 Frag 8 Frag 9 Frag 10 Frag 11 Frag 12 Frag 13 Frag 14 Zn Si N F F C H Units are given in e -. 10

11 Table S4. Partial electrostatic charges on different fragments of SIFSIX-3-Ni. Atom Label Frag 1 Frag 2 Frag 3 Frag 4 Frag 5 Frag 6 Frag 7 Frag 8 Frag 9 Frag 10 Frag 11 Frag 12 Frag 13 Frag 14 Ni Si N F F C H Units are given in e -. 11

12 Table S5. Partial electrostatic charges on different fragments of SIFSIX-3-Cu. Atom Label Frag 1 Frag 2 Frag 3 Frag 4 Frag 5 Frag 6 Frag 7 Frag 8 Frag 9 Frag 10 Frag 11 Frag 12 Frag 13 Frag 14 Cu Si N F F C H Units are given in e -. 12

13 Fragment 1 Fragment 2 Fragment 3 Fragment 4 Fragment 5 13

14 Fragment 6 Fragment 7 14

15 Fragment 8 Fragment 9 15

16 Fragment 10 Fragment 11 16

17 Fragment 12 Fragment 13 17

18 Fragment 14 Figure S4. Illustration of the 14 SIFSIX-3-Zn fragments used to calculate partial charges. Atom colors: Zn = purple, Si = yellow, N = blue, F = cyan, C = gray, H = white. Table S6. Partial electrostatic charges of chemically distict atoms of HUMs. SIFSIX-3-Zn SIFSIX-3-Ni SIFSIX-3-Cu Si F-axial F-equatorial H C N Zn Cu Ni Units are given in e -. 18

19 GCMC calculations were performed using a configurational bias Monte Carlo (CBMC) algorithm 20 implemented in Materials Studio TM sorption module. 21 For this work, we extracted Lennard-Jones interaction parameters from UFF force field. 22 TraPPE force field parameters were used for treating CO 2 as sorbate molecule during all GCMC and MD calculations. 23 The CO 2 molecule was represented as a three site molecule with three partial electrostatic charges fitted to the atomic centers. All GCMC calculations were done in supercell, shown in Figure S1, where the HUMs structure was kept rigid using their experimental structures and with equatorial fluorine atoms at a 45 angle with respect to a- axis based on the results of DFT calculations described previously. For each state point of the adsorption isotherm and isosteric heat of adsorption graphs, GCMC steps were performed to bring the system energy closer to the equilibrium, followed by GCMC steps to allow the system to equilibrate and obtain the final results. The following statistical mechanical definition is numerically calculated during each GCMC step to define the average number of adsorbed molecules:,,,, (5) where, β is 1 in which k is the Boltzmann constant and T is the absolute temperature, µ is the chemical potential of gas reservoir and Ξ is the grand canonical partition function. Peng Robinson equation of state was used to define chemical potential of CO 2 over a range of temperatures. 24 It is important to note, all gas molecules were treated as ideal gases so that the partial pressure was equal to fugacity. Isosteric heat of adsorption (Q st ) was calculated in order to estimate the thermodynamic interactions between sorbate and sorbent. Clausius-Clapeyron equation is used for calculation of Q st over specified ranges of coverage, based on experimentally derived adsorption isotherms. 19

20 (6) where, k is the Boltzmann constant, P is the pressure and T is absolute temperature. Here, Q st is calculated based on the fluctuations of the number of adsorbed molecules and the potential energy during GCMC calculations: + (7) Where, represents the ensemble average number of adsorbed sorbate molecules, is the ensemble average potential energy of the adsorbed phase. K and T are the Boltzmann constant and absolute temperature, respectively. Adsorption Isotherms Carbon dioxide adsorption isotherms for SIFSIX-3-Zn and SIFSIX-3-Cu were calculated using GCMC from 0 to 1 atm at 273 K and 298 K (Figure S5). The CO 2 adsorption isotherms of SIFSIX-3-Ni were calculated at 273 K and 293 K in order to be comparable with the experimental results. In all cases, the simulated isotherms follow the experimental isotherms pattern with good agreement. 20

21 21 (a)

22 22 (b)

23 (c) Figure S5. Simulated and experimental CO 2 adsorption isotherms in (a) SIFSIX-3-Zn, (b) SIFSIX-3-Ni, and (c) SIFSIX-3-Cu. No experimental data was available for SIFSIX-3-Cu at 273 K, although the adsorption isotherm at 298 K is in good agreement with experimental results. Additionally, as is seen in the plots, the SIFSIX-3-Zn structure is approximately saturated with CO 2 at pressures lower than 0.3 atm at both 273 K and 298 K temperatures. The same situation is observed at pressures lower 0.2 atm and 0.1 atm for SIFSIX-3-Ni and SIFSIX-3-Cu, respectively. Saturation at lower partial pressures of CO 2 is attributed to the higher adsorption energy of CO 2 in the two latter HUMs. The saturation adsorption value of CO 2 is essentially constant and similar at pressures higher than 0.3 atm for both calculated temperatures in each of the three HUMs studied. Rapid saturation of these HUMs with CO 2 at extremely low pressures 23

24 portends potential applications of this series of HUMs in CO 2 direct air capture (DAC) as it has been reported in the literature. 25 The saturation value of ca. 2.7 mmol g -1 for each SIFSIX-3-M HUM is ascribed as the presence of only one CO 2 molecule in every pore. Both calculated and experimental adsorption isotherms for all SIFSIX-3-M type variants have the same saturation values at 273 K and 298 K (293 K for SIFSIX-3-Ni) temperatures. Adsorption Sites of CO 2 within SIFSIX-3-Cu and SIFSIX-3-Ni HUMs Density plots, calculated from GCMC, illustrate the distribution of the most energetically favorable CO 2 adsorption sites in a supercell of SIFSIX-3-Zn (Figure S6). Density plots for SIFSIX-3-Ni and SIFSIX-3-Cu are also provided in Figure S7 and Figure S8. From the probability density plots it is clear that CO 2 molecules are more frequently adsorbed in the center of pores, which is attributed to strong electrostatic attraction. In all cases, it was discovered that the preferable adsorption site is just large enough to accommodate a single CO 2 molecule, and for that molecules to be located exactly in the center of the pore equidistant between equatorial fluorine atoms. Furthermore, MD has been exploited to investigate the location and orientation of the CO 2 molecule in the pore (Figure S9). 24

25 (a) (b) Figure S6. Centre of mass probability density of CO 2 at 1 atm fugacity at 273 K in SIFSIX-3-Zn. (a) side view, (b) top view. Atom colors: F = cyan, Zn = purple, Si = yellow, H = white, C = gray, N = blue. (a) Figure S7. Center of mass probability density of CO 2 at 1 atm fugacity at 273 K in SIFSIX-3-Cu. (a) side view, (b) top view. Atom colors: F = cyan, Cu = red, Si = yellow, H = white, C = grey, N = blue. (b) 25

26 (a) Figure S8. Center of mass probability density of CO 2 at 1 atm fugacity at 273 K in SIFSIX-3-Ni. (a) side view, (b) top view. Atom colours: F = cyan, Ni = green, Si = yellow, H = white, C = grey, N = blue. (b) Molecular dynamics calculations were performed using a supercell while the HUM structure is assumed to be rigid, except for the equatorial fluorine atoms. The calculations were made using the same partial charges and force field as the GCMC calculations. The velocity-verlet algorithm was used to integrate Newton s law of motion. First, an 80 ps run was performed in NVT ensemble using 0.5 fs time steps and Nose-Hoover thermostat for equilibration purposes. This was followed by a 100 ps run to collect final results. All MD calculations were done by General Utility Lattice Program (GULP) code. 26 All calculations were conducted at 273 K with the HUMs at saturated condition with one CO 2 molecule in every pore. The sorbate molecules were located in random initial orientations within the pores. 26

27 Figure S9 shows a snapshot of the lowest energy conformation of CO 2 molecules in SIFSIX-3-Zn structure based on MD calculations. The position and orientation of CO 2 molecules in the pores can be explained based on two electrostatic attraction/repulsion forces. Firstly, there is an electrostatic attraction between electropositive carbon atom of sorbate molecule and electronegative equatorial fluorine atoms of the HUMs. The second strong interaction is the electrostatic repulsion between electronegative oxygen atoms of the CO 2 molecule and fluorine atoms of HUMs is also present. Consequently, it is anticipated to locate CO 2 molecules in the center of four equatorial fluorine atoms. Regarding its orientation, it is also expected to be parallel to c-axis of the unit-cell and perpendicular to the equatorial fluorine atoms plane. Note, that the same orientation and location of CO 2 molecule was observed in SIFSIX-3-Cu and SIFSIX-3-Ni compounds. Radial Distribution Function (a) (b) Figure S9. Preferential adsorption sites of CO 2 molecules in SIFSIX-3-Zn, Atom colors: F = cyan, Zn = purple, Si = yellow, H = white, C = gray, N = blue. 27

28 Radial distribution function for the carbon atom of CO 2 around the silicon atom in the pore of each HUM, is depicted in Figure S10. It can be seen that the most probable position of the carbon atom is ca. 4.4 Å to 5.5 Å from the silicon atom, which is nearly in the center of the channels with respect to their diagonal. Also, there is a slight shifting to lower distances between carbon atom and silicon atom from SIFSIX-3-Zn to SIFSIX-3-Ni and SIFSIX-3- Cu, respectively. This is due to the smaller size of the pore and stronger interaction between CO 2 molecule and HUM framework. Figure S10. Radial distribution function of CO 2 carbon atom around a silicon atom of HUM compounds. 28

29 References 1. (a) Subramanian, S.; Zaworotko, M. J., Angew. Chem., Int. Ed. Engl. 1995, 34 (19), ; (b) Noro, S.-i.; Kitagawa, S.; Kondo, M.; Seki, K., Angew. Chem., Int. Ed. 2000, 39 (12), ; (c) Burd, S. D.; Ma, S.; Perman, J. A.; Sikora, B. J.; Snurr, R. Q.; Thallapally, P. K.; Tian, J.; Wojtas, L.; Zaworotko, M. J., J. Am. Chem. Soc. 2012, 134 (8), ; (d) Shekhah, O.; Belmabkhout, Y.; Chen, Z.; Guillerm, V.; Cairns, A.; Adil, K.; Eddaoudi, M., Nat. Commun. 2014, 5; (e) Nugent, P.; Belmabkhout, Y.; Burd, S. D.; Cairns, A. J.; Luebke, R.; Forrest, K.; Pham, T.; Ma, S.; Space, B.; Wojtas, L.; Eddaoudi, M.; Zaworotko, M. J., Nature 2013, 495 (7439), Allen, F., Acta Cryst. 2002, 58 (3 Part 1), (a) Elsaidi, S. K.; Mohamed, M. H.; Schaef, H. T.; Kumar, A.; Lusi, M.; Pham, T.; Forrest, K. A.; Space, B.; Xu, W.; Halder, G. J.; Liu, J.; Zaworotko, M. J.; Thallapally, P. K., Chem. Commun. 2015, 51 (85), ; (b) Shekhah, O.; Belmabkhout, Y.; Adil, K.; Bhatt, P. M.; Cairns, A. J.; Eddaoudi, M., Chem. Commun. 2015, 51 (71), Uemura, K.; Maeda, A.; Maji, T. K.; Kanoo, P.; Kita, H., Eur. J. Inorg. Chem. 2009, 2009 (16), Blöchl, P. E., Phys. Rev. B 1994, 50 (24), Giannozzi, P.; Baroni, S.; Bonini, N.; Calandra, M.; Car, R.; Cavazzoni, C.; Ceresoli, D.; Chiarotti, G. L.; Cococcioni, M.; Dabo, I., J. Phys.: Condens. Matter 2009, 21 (39), Perdew, J. P.; Burke, K.; Ernzerhof, M., Phys. Rev. Lett. 1996, 77 (18), 3865.

30 8. Vanderbilt, D., Phys. Rev. B 1990, 41 (11), Monkhorst, H. J.; Pack, J. D., Phys. Rev. B 1976, 13 (12), Grimme, S., J. Comput. Chem. 2006, 27 (15), Hobza, P.; šponer, J.; Reschel, T., J. Comput. Chem. 1995, 16 (11), Jones, J. E., Proc. R. Soc. London, Ser. A 1924, 106 (738), (a) Lorentz, H. A., Ann. Phys. (Berlin, Ger.) 1881, 248 (1), ; (b) Bertholt, D., Comptes rendus hebdomadaires des séances de l Académie des Sciences 1898, (126), (a) Ewald, P. P., Ann. Phys. (Berlin, Ger.) 1921, 369 (3), ; (b) Fennell, C. J.; Gezelter, J. D., J. Chem. Phys. 2006, 124 (23), Valiev, M.; Bylaska, E. J.; Govind, N.; Kowalski, K.; Straatsma, T. P.; Van Dam, H. J. J.; Wang, D.; Nieplocha, J.; Apra, E.; Windus, T. L.; de Jong, W. A., Comput. Phys. Commun. 2010, 181 (9), Breneman, C. M.; Wiberg, K. B., J. Comput. Chem. 1990, 11 (3), (a) Ditchfield, R.; Hehre, W. J.; Pople, J. A., J. Chem. Phys 1971, 54 (2), ; (b) Hariharan, P.; Pople, J. A., Mol. Phys 1974, 27 (1), ; (c) Hehre, W. J.; Ditchfield, R.; Pople, J. A., J. Chem. Phys 1972, 56 (5), (a) Hay, P. J.; Wadt, W. R., J. Chem. Phys 1985, 82 (1), ; (b) Hay, P. J.; Wadt, W. R., J. Chem. Phys 1985, 82 (1), ; (c) Wadt, W. R.; Hay, P. J., J. Chem. Phys 1985, 82 (1),

31 19. Forrest, K.; Pham, T.; Hogan, A.; McLaughlin, K.; Tudor, B.; Nugent, P.; Burd, S.; Mullen, A.; Cioce, C.; Wojtas, L.; Zaworotko, M.; Space, B., J. Phys. Chem. C 2013, 117 (34), Siepmann, J. I.; Frenkel, D., Mol. Phys. 1992, 75 (1), Akkermans, R. L.; Spenley, N. A.; Robertson, S. H., Mol. Simul. 2013, 39 (14-15), Rappe, A. K.; Casewit, C. J.; Colwell, K. S.; Goddard, W. A.; Skiff, W. M., J. Am. Chem. Soc. 1992, 114 (25), Potoff, J. J.; Siepmann, J. I., AIChE J. 2001, 47 (7), Peng, D.-Y.; Robinson, D. B., Ind. Eng. Chem. Fundam. 1976, 15 (1), Kumar, A.; Madden, D. G.; Lusi, M.; Chen, K.-J.; Daniels, E. A.; Curtin, T.; Perry IV, J. J.; Zaworotko, M. J., Angew. Chem., Int. Ed. 2015, 54 (48), Gale, J. D., J. Chem. Soc., Faraday Trans. 1997, 93 (4),