This doctoral thesis presents a thorough computational investigation into the atomic-scale structure and adsorption behavior of natural clinoptilolite, a widely available and industrially relevant zeolite. Though it is practically important in water treatment, catalysis, and drug delivery, clinoptilolite remains underexplored at the atomistic level, especially regarding its surface properties, cation distribution, and interaction mechanisms with large pharmaceutical molecules. Addressing this gap, the present work develops and applies a multi-layered, reproducible modeling framework that combines dispersion-corrected density functional theory (DFT-D3) and classical molecular dynamics (MD) to study aluminum placement, extra-framework cation distribution, surface termination, and molecule–surface adsorption phenomena in mono- and multi-cationic clinoptilolite systems. The study begins with the generation of periodic bulk models including experimentally guided aluminum distributions and extra-framework cation arrangements (Na+, Ca2+, K+, and their combinations)—element-to-site assignments dictated with DFT-D3 calculations—while strictly adhering to Loewenstein’s rule. Motivated by the need for reproducible and accurate DFT simulations, an extensive comparison of nine exchange-correlation functionals was conducted, leading to the selection of the B97-D3 functional as the most robust for clinoptilolite systems. The framework also introduces improved basis sets, especially for Ca2+, to better capture its coordination environment. Cation site preferences were evaluated, and it turns out that Na+ favored Al at T2 and T3 and localized mainly in channels A and B, Ca2+ was stabilized in channel B and coordinated with Al at all T sites, while K+ preferred the narrower channel C and favored Al at T1 and T3. These observations validate known experimental trends and offer reliable benchmarks for future modeling. Overall, framework stability was shown to depend critically on both the Al distribution and the identity of the charge-balancing cation. The next part of the study focused on modeling the external surfaces of Na–clinoptilolite and their interaction with 5-fluorouracil as a model pharmaceutical compound. A hybrid sampling approach was employed, combining simulated annealing (SA) and parallel tempering (PT) molecular dynamics for initial exploration of adsorption motifs, followed by DFT-D3 refinement of selected low-energy configurations. Adsorption energies spanned a broad and significant range (from –430.0 to –174.4 kJ/mol), with configurations featuring exposed Na+ cations showing regularly stronger binding. Contrary to Na+’s steric limitations in the bulk, surface-bound Na+ was found to play an active role in anchoring 5-FU via Na–O and Na–F interactions, further reinforced by hydrogen bonding with the framework or hydroxyl oxygens. Among various terminations, surfaces exposing 8-membered rings (8MR) consistently yielded stronger adsorption compared to 10MR-exposed surfaces, due to enhanced confinement and more favorable H-bonding geometry. Cation-free surfaces showed significantly weaker interactions, which highlights the critical role of surface composition and local electrostatics. Building upon these insights, the adsorption study was extended to Ca–, Na–Ca–, and Na–Ca–K–clinoptilolite systems. Using the same hybrid MD/DFT strategy, the final part of the investigation comprehensively broke down and examined the competitive and cooperative behavior of multiple cations in driving molecular adsorption. A clear energetic trend was observed: Na–Ca–K > Na > Ca > Na–Ca, and it was indicated that adsorption strength is governed not merely by cation charge or size, but by a combination of cooperative interactions and spatial arrangement. Interestingly, configurations where Ca2+ alone coordinated with the adsorbate often outperformed those with multiple cations directly involved, which suggests that the spatial separation of cations and the resulting local electrostatic environment can outweigh simple additive cation effects. Moreover, cations that are not coordinating with the molecule directly such as K+ and Na+ were found to enhance adsorption indirectly by modulating the local electrostatic environment. Al distribution asymmetry was also shown to influence adsorption, with uneven Al placement enhancing surface anionic character and thus improving cation anchoring and molecule binding. Altogether, this thesis provides deep mechanistic insight, quantitative adsorption energies, and significant structural comparisons that are fully reproducible through the provided computational framework and accompanying scripts. The study demonstrates that clinoptilolite surface reactivity is governed by a delicate balance of Al–cation configuration, surface accessibility, and molecular complementarity (how well the molecule “fits” or “matches” the surface), offering a new paradigm for tuning zeolite-based adsorbents through cation engineering. This work not only fulfills but also extends the original aims of the project proposal, which sets a computational benchmark for future studies in zeolite surface modeling and bridges the gap between structural complexity and adsorption performance in natural materials.
Lobna Saeed (Fri,) studied this question.