In a recent molecular dynamics study [1] in collaboration with Prof. K. J. Karki (Department of Physics, Guangdong Technion-Israel Institute of Technology in China), we explored how EthylChlorophyllide a behaves when confined between two silica surfaces — a situation relevant for artificial photosynthesis, nanomaterials, and bio-inspired light-harvesting systems. Chlorophylls are among the most important molecules on Earth. They enable plants, algae, and photosynthetic bacteria to convert sunlight into chemical energy. Yet, outside their natural protein environment, chlorophyll molecules are fragile as they can easily lose their central magnesium ion (demetallation), they degrade under light, and they tend to aggregate uncontrollably in solution.

In natural photosynthetic systems, proteins protect and organize chlorophylls. Reproducing this level of control in artificial systems remains a major challenge. One promising strategy is nanoconfinement — trapping chlorophyll derivatives inside well-defined inorganic structures such as silica nanopores.

The Model System: Chlorophyll Between Two Walls

In our study, we focused on EthylChlorophyllide a (EChlideA), a chlorophyll a derivative frequently used in experiments due to its enhanced chemical stability. Using molecular dynamics (MD) simulations, we modeled a methanol solution confined between two hydroxylated silica surfaces, separated by about 4 nm, comparable to experimental silica nanoslits. We have studied systems containing 1, 2, or 4 EChlideA molecules, simulated for 1 microsecond at room temperature (298 K). This allowed us to observe how molecular crowding and confinement affect adsorption, orientation, and motion at the atomic level.

Strong Attraction to Silica Surfaces

One of the most striking results is that EChlideA molecules strongly adsorb onto the silica surfaces. The interaction is driven primarily by specific contacts between the chlorin ring (especially methyl groups) and the surface hydroxyls of silica. Once adsorbed, molecules remain bound for long times, particularly at low concentration. Potential of Mean Force (PMF) calculations confirm that adsorption is energetically favorable. At higher concentrations, binding becomes more heterogeneous due to molecular aggregation and competition for surface sites.

Orientation Matters: Flat Is Preferred

When bound to silica, EChlideA molecules do not orient randomly. The chlorin ring tends to lie parallel to the surface. Surface diffusion requires rotational adjustments, indicating that motion is constrained not only translationally but also orientationally. This preferred alignment may be important for controlling optical coupling in artificial light-harvesting assemblies.

Despite strong confinement and surface binding, the magnesium ion at the center of the chlorin ring remains properly coordinated by solvent molecules, similar to bulk methanol; only modest changes are observed at higher pigment concentrations. This is an interesting result, as magnesium loss is one of the key degradation pathways for chlorophylls.

Slower Motion, Longer Lifetimes

Confinement has a clear impact on molecular dynamics by reducing the Linear diffusion compared to bulk solution, and incresing the Rotational relaxation times, especially at higher pigment concentrations. In simple terms, the molecules move less and rotate more slowly — a condition that may reduce the probability of photochemical damage.

Implications for Artificial Photosynthesis

These findings help explain why chlorophyll derivatives confined in silica nanopores are often found to be more stable experimentally. They suggest that silica nanostructures can immobilize pigments without disrupting their coordination chemistry, control aggregation, and enforce favorable orientations. This combination is highly desirable for artificial photosynthetic systems, nanoscale photonic devices, and pigment-based sensors.

REFERENCE

[1] D. Roccatano, K. J. Karki.  A Molecular Dynamics Simulation Study of EthylChlorophyllide a Molecules Confined in a SiO2 Nanoslit. J. Chem. Phys. 161, 144703 (2024). DOI: https://doi.org/10.1063/5.0233264

The article was part of the special collection dedicated to Molecular Dynamics, Methods and Applications 60 Years after Rahman.