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Molecular motion in confined systems

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As part of the European Cooperation in Science and Technology, or COST Action, Working Group 2 of the COSY network focuses on developing efficient methods for describing the motion of molecules in confined systems.

Their work covers four key areas, ranging from toxic gas separation to tumour biomarker detection.

Find out more about the COSY COST Action network on cost-cosy.eu 

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Hello and welcome to ResearchPod. Thanks for listening and joining us today. In this episode, we are talking about an interdisciplinary research network named Confined Molecular Systems: From a New Generation of Materials to the Stars, also known as COSY, which recently celebrated its second anniversary. As part of the European Cooperation in Science and Technology, or COST Action, Working Group 2 of the COSY network focuses on developing efficient methods for describing the motion of molecules in confined systems. 

This working group brings together about 150 leading experts across a variety of fields, spanning four key areas. The first of these considers the properties of porous adsorbent materials such as metal-organic frameworks and covalent organic frameworks, with a focus on the capture and separation of toxic gases. 

A second area focuses on simulating the dynamics of confined biomolecules such as nucleic acids and proteins. This could lead to promising applications in technologies such as gene delivery, as well as the design of bioactive molecules, which include antiviral drugs.

Researchers in the third area investigate the applications of metal clusters in biological environments. In particular, the researchers consider the possible use of these clusters as nonlinear optical contrast agents for detecting tumour biomarkers. Finally, a fourth group is focusing on modelling nuclear quantum effects and nonadiabatic dynamics in confined systems.


One notable project is led by Dr Sonja Grubišić from the University of Belgrade, together with Professor Majdi Hochlaf from the University of Paris: part of a long-standing collaboration between researchers in France, Serbia, and Tunisia. Their paper has been published in Physical Chemistry Chemical Physics, and even appeared on the journal’s front cover.

The team’s research focuses on designing and characterizing metal-organic frameworks, or MOFs, for the purpose of capturing and sequestering pollutants and toxic gases. By studying these materials from first principles, the team has developed a multiscale procedure to study how gases like carbon dioxide and sulphur compounds will interact with MOFs: a process primarily driven by hydrogen bonds and van der Waals forces. Additionally, they  used Grand-Canonical Monte Carlo simulations to predict gas adsorption isotherms.

The calculations revealed that while these interactions are universal, they are still weak. In this study, Grubišić, Hochlaf, and their colleagues demonstrated that sulphur dioxide and hydrogen sulphide are strongly adsorbed by the zinc triazolate framework, MAF-66. 

What’s more, they showed that by modifying this MOF into a new zinc triazolate framework, labeled as ZTF, they could enhance its ability to capture these gases. This in-silico approach is not only predictive but also highly beneficial: significantly reducing the cost of experiments, eliminating the need to handle dangerous chemical compounds, and aiding in the development of next-generation materials. 


Another collaboration involved research teams from Germany and Estonia, led by Dr. Kaido Sillar from Tartu University and Prof. Joachim Sauer from Humboldt University in Berlin. Together, the group produced a paper in the Journal of Chemical Physics, titled Ab Initio Prediction of Adsorption Selectivities for Binary Gas Mixtures on a Heterogeneous MOF Surface.

The study focused on how gas separation processes could be improved, which will be crucial for applications including carbon capture and storage, as well as biogas upgrading. Traditionally, these applications involve energy-intensive methods like cryogenic distillation and amine scrubbing, making porous solids like MOFs an especially promising alternative. 

In their study, Sillar and Sauer’s group used Grand Canonical Monte Carlo simulations to predict adsorption selectivities for various gas mixtures, including carbon dioxide, methane, and nitrogen in a metal-organic framework known as Mg-MOF-74. 

Their findings suggest that while vacuum swing adsorption is ideal for methane purification, pressure swing adsorption works best for separating carbon dioxide and nitrogen. However, Mg-MOF-74 showed no significant selectivity for mixtures of methane and nitrogen. The study also found that the Ideal Adsorbed Solution Theory tends to underestimate selectivities for non-ideal adsorbed phases, indicating that real-world materials could perform better than theoretical predictions.

Another breakthrough within COSY’s framework has investigated how molecules like DNA will interact with various substances in confined environments. The research involves a collaboration between researchers from Italy, Sweden, Ukraine, and Romania, led by Dr. Francesca Mocci from the University of Cagliari, and Dr. Sergiy Perepelytsya from Kyiv University. Their findings have been published in several international journals, including Journal of Molecular Liquids, Low Temperature Physics, and Frontiers in Chemistry.

Through their research, the group are shedding new light on how small, flexible polyamine molecules such as spermidine can be confined within DNA, and considers various effects that are crucial for biological and technological applications. With their systematic and multifaceted computational approach, they are currently unravelling the complex structural space of these interacting molecules. 

So far, Mocci, Perepelytsya, and their colleagues have demonstrated how the concentration, molecular crowding, and confinement of these molecules can lead to significant and previously undiscovered molecular organizations, and have also clarified how this structural complexity can be rationalized within a limited set of molecular conformations. 

While some molecular processes can be described using classical molecular dynamics, others require quantum molecular dynamics, which involves solving the time-dependent Schrödinger equation. For a molecule with 20 atoms, this leads to a 60-dimensional wavefunction, making an exact solution both computationally impractical and difficult to interpret.


Semiclassical approximations provide a practical alternative, capturing key quantum effects such as phase and interference, while remaining feasible for larger systems and easier to interpret. In a recent Journal of Chemical Physics paper, Prof. Jiří Vaníček from the Ecole Polytechnique Fédérale de Lausanne extended one of the simplest semiclassical methods, which approximates the wavefunction using a multi-dimensional Gaussian wavepacket. He demonstrated that well-known methods, such as thawed and variational Gaussian approximations, belong to a larger family of Gaussian wavepacket dynamics. Each of these methods provides an exact solution to a nonlinear Schrödinger equation with a locally quadratic effective potential. Vaníček also showed that this family includes an infinite number of other methods, forming a hierarchy that allows researchers to balance accuracy and computational cost, and to select the approach best suited to their computational resources.


In collaboration with Prof. María Pilar de Lara Castells’ group, the AbinitSim Unit at the Institute of Fundamental Physics in the Spanish National Research Council  in Madrid  (CSIC) , Vaníček’s group is further investigating nonadiabatic effects on the oxidation of copper clusters, which are promising catalysts for CO₂ (photo)reduction, on the basis of de Lara-Castells’ group and co-workers' studies. Nonadiabatic effects arise when the Born-Oppenheimer approximation breaks down, allowing the nuclei of the cluster to jump between surfaces with different electronic potential energy, altering the forces that drive their motion. PhD student Yeha Lee from Lausanne is employing advanced nonadiabatic quantum dynamics techniques to simulate charge transfer reactions between oxygen molecules and a copper cluster. Her goal is to uncover how these effects influence the resistance of copper clusters to oxidation.


In a collaborative study led by Prof. Martin Quack from ETH Zurich and Prof. Michael Hippler from Sheffield University, COSY researchers have made important advances in our understanding of hydrogen bonding. Their groundbreaking results were published in Molecular Physics and the Israel Journal of Chemistry.

Hydrogen bonding provides a subtle yet crucial force that holds molecules together and plays a vital role in nature. It is the reason water is liquid at ordinary temperatures, and why biomolecules in the genetic code can recognize and bind to each other selectively – yet gently enough to allow for separation when needed. Understanding hydrogen bonding at the quantum level presents a fundamental challenge.

Using very high-resolution spectroscopic experiments across a wide range of energies,  Quack and Hippler’s team demonstrated the important role of the quantum mechanical tunnel effect in hydrogen-bonded dimers of hydrogen fluoride, a simple yet prototypical example of hydrogen bonding. 

The researchers showed that the rearrangement, or switching of the hydrogen-bonded structures and the dissociation process breaking the hydrogen bond are highly mode-selective, with large quantum effects. These effects cannot be described by the classical dynamics commonly used in molecular and biomolecular simulations.


Finally, if you’ve ever wondered what happens when molecules interact with light, Professor Leticia Gonzalez from Vienna University and her team are at the forefront of providing answers. Their research sits at the intersection of quantum mechanics and classical physics.

In their lab, the researchers explore how the motion of atoms comes into play when molecules absorb light. When certain molecules absorb light, their electrons become energized, pushing the whole system out of equilibrium. These excited molecules can then undergo chemical reactions that wouldn’t be possible otherwise.

To study this, Prof. Gonzalez's group combines the precision of quantum chemistry with the efficiency of classical physics. Think of it as watching a dance between light and matter, with each step crucial to understanding how things like artificial photosynthesis or new photocatalysts could work. By simulating these interactions, the team is aiming to help design materials better suited for renewable energy.

When molecules are confined in larger structures, like biological membranes or synthetic DNA scaffolds, they use a divide-and-conquer approach, treating the environment classically while focusing on the quantum interactions inside. This allows them to simulate larger systems over longer timescales with remarkable accuracy.


The leaders of Working Group 2, Sonja Grubišić and Jiří Vaníček,  would like to express their gratitude to all the colleagues and friends who have contributed to the success of the COSY project. Special thanks go to Action Chair Maria Pilar de Lara Castells for her outstanding leadership and dedication throughout this initiative.


Thanks very much for listening. You can find out more about the COSY COST Action network on the website cost-cosy.eu. Stay subscribed to ResearchPod for more of the latest science. See you again soon.