A dispersion-corrected density-functional theory study of small molecules adsorbed in alkali-exchanged chabazites

Tris(o-phenylenedioxy)cyclotriphosphazene (TPP) became the compound of choice to investigate the structural features of organic zeolites and their potential applications as soft materials. A van der Waals crystal of the TPP analogue (host) with the thiophene side fragment tris(3,4-thiophenedioxy)cyclotriphosphazene (TTP) was designed to investigate the selective adsorption among some common gases (guest): methane (CH(4)), carbon dioxide (CO(2)), nitrogen (N(2)), or hydrogen (H(2)). The crystal structure of TTP was modeled by applying minimization methods using the COMPASS (condensed-phase optimized molecular potentials for atomic simulation studies) force field. Interaction energies and structural properties of van der Waals complexes of the crystal of TTP and gas molecules were studied using the dispersion corrected density functional theory (DFT-D). The proper functional and basis set were selected after comparing with benchmark data of the coupled-cluster calculations with singles, doubles, and perturbative triple excitations [CCSD(T)] estimated at the complete basis set (CBS) limit. On the basis of our results, the interaction energy between the host and the guest molecules was predicted in the increasing order of host-H(2) << host-N(2) < host-CH(4) < host-CO(2), suggesting the designed TTP is a good candidate as an organic zeolite for potential fuel storage, hydrogen purification, carbon dioxide removal from the air, as well as safety care in a coal mine.

Porous aluminophosphates (AlPOs) and silicoaluminophosphates (SAPOs) with zeolite-like structures have received considerable attention as potential adsorbents for heat transformation applications using water adsorption/desorption cycles. Since a detailed experimental characterisation of the water adsorption properties has only been performed for some of these materials, such as AlPO-18 (AEI topology) and SAPO-34 (CHA topology), more systematic insights regarding the influence of the pore topology and (for SAPOs) the arrangement of the framework protons on the affinity towards water are lacking. To study the relationships between structure and properties in more detail, the interaction of water with six structurally different AlPOs (with AEI, AFX, CHA, ERI, GIS, RHO topologies) and their SAPO analogues was investigated using dispersion-corrected density-functional theory (DFT-D) calculations. Different possible locations of silicon atoms and charge-balancing protons were considered for the SAPO systems. The calculations for SAPOs at low water loadings (one H2O molecule per framework proton) revealed that the interaction energies exhibit a considerable variation, ranging from −75 to −100 kJ mol−1 (per water molecule). The differences in interaction energy were rationalised with the different structural environment of the framework protons at which the water molecules are adsorbed. At high water uptakes (near saturation), interaction energies in the range of −65 kJ mol−1 were obtained for all AlPOs, and there was no evidence for a marked influence of pore size and/or topology on the interaction strength. The interaction of water with SAPOs was found to be approximately 5 kJ mol−1 stronger than for AlPOs due to an increased contribution of electrostatic interactions. An analysis of the structural changes upon water adsorption revealed striking differences between the distinct topologies, with the materials with GIS and RHO topologies being distorted much more drastically than the systems based on double six-ring (d6r) units. Moreover, the direct coordination of water molecules to framework aluminium atoms occurs more frequently in these materials, an observation that points towards a reduced structural stability upon hydration.

Investigation of zinc binding properties onto natural and synthetic zeolites: Implications for soil remediation

Limits to Paris compatibility of CO2 capture and utilization

Ionic liquids (ILs) hold great promise in many fields including energy storage and generation, mechanical, pharmaceutical, synthetic and separation applications to name just a few. For any given application, the desired physical properties of the ideal IL may differ substantially from others and no widely applicable patterns or trends to facilitate intuitive design. The origins of physical properties lie in the characteristics of the intermolecular energetics, which consist of a complex interplay between electrostatic and dispersion forces. This thesis investigates and develops computational methodologies for calculating a reliable description of the intermolecular interactions for this challenging class of solvents and electrolytes of the future. The electrostatic approximation used in classical molecular dynamics (MD) where atomic partial charges are assigned was investigated in terms of methods based on density matrix partitioning, and the restrained electrostatic potentials (RESP) approaches. It was found that the “geodesic” atomic partial charge scheme, part of the RESP family, produced the most accurate charges. This was measured in terms of (a) charge convergence with increasing basis set size; (b) charge invariance with changes to the coordinate system; (c) insensitivity to minor structural changes on the resulting charges; (d) adequate capture of charge transfer effects; and (e) the preservation of symmetric of charges in symmetric molecules. Although charges can vary dramatically depending on the scheme used, the careful use of atomic partial charge schemes may still produce reliable forcefields, or at least serve as a rapid diagnostic tool to quantify electrostatic interactions and charge transfer. In moving towards unbiased a priori descriptions of IL intermolecular interactions, second-order Moller-Plesset perturbation theory (MP2) was used with the linear-scaling fragment molecular orbital (FMO) framework to assess the extent to which dispersion forces play a role in the intermolecular energetics. ILs of increasing size were examined such that the many-body effects may be captured. The dispersion energy contribution formed up to 20% of the total interaction energy. Furthermore, the interaction energy as produced by FMO was within 1 kJ mol−1 of the full-wavefunction MP2 interaction energy when three-body effects were included. As the dispersion interaction is purely a quantum mechanical phenomenon, correlated quantum mechanical methods, such as MP2 or coupled-cluster approaches, are required to provide an unbiased account of these effects. Ab initio methods such as MP2 and CCSD(T) scale formally as N⁵ an N⁷, respectively, with chemical system size. While the FMO approach provides a marked improvement in efficiency, the counterpoise (CP) approach to correcting the basis set superposition error (BSSE) is not amenable to fragmented approaches and requires each ion in the cluster to be calculated in the basis set of the entire system. In order to remove this bottleneck, the spin-component scaled second-order Moller Plesset perturbation theory (SCS-MP2) methodology was refined by fitting 174 non-CP corrected interaction energies at the MP2/cc-pVTZ level of theory to CP corrected CCSD(T)/CBS benchmark energies. This has resulted in an implicit BSSE correction that may be used within the highly efficient FMO framework, and is shown to yield results on par with or exceeding the accuracy of MP2/cc-pVQZ for clusters of two and four ion pairs (IPs). This new approach as been termed SCS-IL-MP2. An alternative dispersion corrected density functional theory (DFT) approach, DFT- D3, was assessed and refined in view of producing accurate interaction energies at the same CCSD(T)/CBS quality. The same test set of 174 ILs was used to fit the SCS-IL-MP2 approach was used to refit the DFT-D3 approach for both the Hartree-Fock (HF) wavefunction and the PBE and BLYP density functionals (DFs). In most cases, the selection of the DF and associated DFT-D version 3 (DFT-D3) parameters differed negligibly with all reaching within 1 to 2 kJ mol−1 per IP. HF-D3 parameters, on the other hand, showed a substantial improvement, particularly when used with the Becke-Johnson (BJ) damping function. Refitted HF-D3 and the BJ damping function was able to consistently provide interaction energy errors below 5 kJ mol−1 per IP. It would be worthwhile further investigating the application of the refined HF-D3 in its ability to produce reliable energies and geometries over a more diverse set of ILs. Both the SCS-IL-MP2 and new DFT-D3 approaches may be applied to the highly scal- able FMO framework. These form the core elements of the quantum chemistry toolbox for the study and understanding of the physicochemical properties of ILs that have so far been only superficially characterised by electronic structure theory. From this starting point, a rigorous and unbiased a priori understanding of the intermolecular interactions and resulting physicochemical properties may be predicted by means of efficient ab initio molecular dynamics (AIMD) techniques.

Ab-Initio MODPOT SCE calculations using our own optimized well-balanced minimal basis sets have little basis set superposition error (BSSE) and have proven over the years to give reliable intermolecular geometries and interaction energies. Another approach, using ab initio potential functions from energy partitioned ab initio calculations, has also yielded reliable interaction energies and intermolecular geometries, including crystal structures. We used both of these techniques in comparing the results of a published large all-electron basis set calculation on the nitromethane dimer with the above methods. Our SCF intermolecular minimum energy was at the same internuclear distance as the large all-electron basis set. Our SCF interaction energy, corrected for BSSE, was only 0.4 kcal above the SCF energy of the large basis set SCF calculation corrected for BSSE. We also calculated the energy partitioned components with our ab initio MODPOT basis set and with the larger all-electron basis set and showed that the small difference in interaction energy was due to a small difference in the first-order electrostatic multipolar term. (We also calculated this term from correlated wave functions [SDQ-MBPT (4)] using both ab initio MODPOT and the larger all-electron basis sets). From values of the first-order electrostatic multipolar term from SCF and correlated monomer wave functions, the contribution to intermolecular interaction energy due to the use of correlated monomer wave functions has been estimated. Our results indicate either the dominant role of electrostatic term or near cancellation of the remaining components of intermolecular interaction energy. For cyclic nitromethane dimer at equilibrium distance these effects approach 0.9 kcal/mol (nearly 1/4 of total interaction energy). In addition, we showed that the semitheoretical expression and parameters we use for estimating the dispersion energy gave results very close to the published variation perturbation results from the larger basis set calculation.

Serotonin transporter (SERT) is the main target for widely used antidepressant agents. Several of these drugs, including imipramine, citalopram, sertraline, and fluoxetine (Prozac), bound more avidly to SERT in the presence of Cl(-). In contrast, Cl(-) did not enhance cocaine or paroxetine binding. A Cl(-) binding site recently identified in SERT, and shown to be important for Cl(-) dependent transport, was also critical for the Cl(-) dependence of antidepressant affinity. Mutation of the residues contributing to this site eliminated the Cl(-)-mediated affinity increase for imipramine and fluoxetine. Analysis of ligand docking to a single state of SERT indicated only small differences in the energy of interaction between bound ligands and Cl(-). These differences in interaction energy cannot account for the affinity differences observed for Cl(-) dependence. However, fluoxetine binding led to a conformational change, detected by cysteine accessibility experiments, that was qualitatively different from that induced by cocaine or other ligands. Given the known Cl(-) requirement for serotonin-induced conformational changes, we propose that Cl(-) binding facilitates conformational changes required for optimal binding of fluoxetine and other antidepressant drugs.

Monte Carlo simulations are carried out to compute the solubility of SO2, O2, and N2 in the ionic liquid 1-n-hexyl-3-methylimidazolium bis(trifluoromethylsulfonyl)amide ([hmim][Tf2N]). Simulations are also used to compute the mixed gas isotherms for the mixtures CO2/O2, SO2/N2, and CO2/SO2. The pure gas isotherms agree well with available experimental data. For the mixtures CO2/O2 and SO2/N2, the simulations predict that the mixed gas solubilities are nearly ideal, with little enhancement or competition between the two solutes. This is contrary to published experimental studies, which found that in a gas mixture, CO2 enhances the solubility of the otherwise sparingly soluble O2 and that the poorly soluble N2 inhibits the solubility of the highly soluble SO2. For the SO2/CO2 mixture, it is found that the two gases absorb independently at low pressure but compete with one another at high pressure. An energetic analysis was performed for the different solutes in the ionic liquid. The van der Waals energy between the solutes and ionic liquid was greater than the electrostatic interactions, and the van der Waals interactions were roughly the same between the solutes and the two different ions. CO2 and SO2 interact more strongly with the anion than the cation due to stronger electrostatic interactions between the solute and the anion. N2 and O2 interact weakly with the ionic liquid and show little difference in interaction energy between the cation and anion. Regular solution theory (RST) was evaluated for its ability to predict pure and mixed gas isotherms. It was found that if RST was applied in a strictly predictive mode using experimentally derived parameters, solubilities of CO2 were underpredicted by a substantial margin.

Preliminary Assessment of Tuff as CO2 Sorbent

We carried out ab initio fragment molecular orbital calculations for wild-type and halogenated glutathione S-transferase (GST) at the MP2/6-31G** level. To elucidate the mechanism of structural stability of the halogenated protein, we calculated the interaction energies for all residue pairs in GST by using inter-fragment interaction energy analysis based on the fragment molecular orbital method. We were able to evaluate electrostatic and van der Waals dispersion interaction energies separately and explicitly. Differences in interaction energies of each residue pair between the two structures were interpreted as the effect of halogenation. The results show that the local interaction around halogen atoms was enhanced. The enhanced interaction effects of Cl and Br were stronger than those of F and I.

The potential of direct air capture using adsorbents in cold climates.

Contrary to the conclusions based on isotropic elasticity, anisotropic elasticity theory predicts that a screw dislocation in the b.c.c. lattice dissociated symmetrically into three 1/6 [111] partial dislocations on {110} planes is stable or metastable. A symmetric dissociation on {112} planes is unstable. For the highly anisotropic alkali metals the threefold symmetrically dissociated stable configuration on {110} has a lower interaction energy than the asymmetric dissociation considered by Sleeswyk (1963). This is consistent with the 3-fold symmetrically dissociated structure for sodium found by atomistic simulations. For the less anisotropic b.c.c. transition metals the sign of the energy difference is reversed, but the total fault energy for the symmetric structure is lower than for the Sleeswyk configuration by an amount estimated to be larger than the interaction energy difference. For an asymmetric configuration with the third partial off-centre, the interaction energy difference will be smaller and may be outweighed by a larger self energy of this partial. The symmetric configuration (dissociated on {110} planes) may then have a lower total energy than either of the asymmetrical configurations, which is consistent with the predictions of several atomistic simulations of the core structure of the screw dislocation for b.c.c. transition metals.

High‐flow nasal therapy – modelling the mechanism

Membrane technology in carbon dioxide removal

Zeolite materials are among the relatively cheap and readily available materials for wastewater treatment. However, the performance of zeolite-based systems can be highly affected by the material properties. In this study, the treatment system based on natural zeolite materials from Chankanai mines in Kazakhstan was compared with a synthetic zeolite treatment system for the purification of groundwater. Water quality indices were also developed from a set of selected water quality parameters to further assess the state of water quality of raw groundwater and the effluents treated with natural and synthetic zeolite. The lowest removal efficiency of natural zeolite (30%) was observed with zinc, while the lowest removal efficiency (36%) of synthetic zeolite was observed with arsenic. With turbidity and beryllium, we observed the maximum removal efficiency (100%) of natural zeolite, whereas with turbidity, we observed the highest removal efficiency (100%) of synthetic zeolite. When the groundwater samples were put through the natural zeolite treatment system, removal efficiency of 50% and above was obtained with 27 (79.4%) out of the 34 water quality parameters examined. On the other hand, when the groundwater samples were put through the synthetic zeolite treatment system, more than 50% removal efficiency was attained with 30 (88.2%) out of the 34 water quality parameters studied. The aggregated water quality index of raw groundwater was 3278.24, falling in the “water unsuitable for drinking” category. The effluent treated with natural zeolite generated 144.82 as a water quality index, falling in the “poor water” quality category. Synthetic zeolite generated 94.79 as a water quality index, falling in the “good water” quality category. Across the board, it was shown that the synthetic zeolite treatment system outperformed the natural zeolite treatment system according to a number of water quality parameters. The findings of this study offer substantial knowledge that can be used to develop more efficient groundwater treatment technologies.