Report
Teaser, summary, work performed and final results
Periodic Reporting for period 2 - DYNAPORE (Dynamic responsive porous crystals)
Teaser
The materials that society relies on to maintain and enhance living standards are produced by chemical manufacturing. Modern chemical manufacturing relies on solid porous materials for many key steps that involve the separation of molecules and/or their chemical...
Summary
The materials that society relies on to maintain and enhance living standards are produced by chemical manufacturing. Modern chemical manufacturing relies on solid porous materials for many key steps that involve the separation of molecules and/or their chemical transformations by catalytic processes. These solid porous materials, such as zeolites and carbons, have rigid solid state structures that are optimisable only for one chemical operation. This strongly contrasts with the natural manufacturing of chemicals in living systems, which perform complex processes at ambient conditions efficiently and selectively in single unit operations that combine multiple chemical steps. Nature can do this because it has access to dynamic, soft materials (such as proteins, DNA, polysaccharides etc.) that can respond to their chemical environments at each point in the process. For example, catalysis in biological systems is performed by the class of proteins known as enzymes. Proteins are chains of amino acids connected by peptide bonds. Many proteins are characterised by the potential availability of multiple structures, in strong contrast to the rigid porous materials used in current chemical manufacturing. These structures are related to each other by changes in single bond rotations of their polypeptide backbone. The appropriate structure for a particular chemical function, such as the binding or release of a specific molecule at a particular point in a more complex process, can then be selected by chemical stimulus provided by the environment, such as a change in the species interacting with the protein. This stimulus would change the protein structure by changing the rotations about the bonds that define the protein structure.
If we could design and produce porous materials that dynamically select the appropriate structure to carry out a desired chemical function in response to their environment, we would be able to manufacture, manipulate and deliver molecules in an entirely new way which builds in the efficiency of biological systems, reduces the operational cost of the chemical industry and improves its environmental footprint.
The overall objective of the project is to produce synthetic flexible porous materials that can adopt multiple structures, which are interconnected by the same single bond rotation pathway that proteins use, and to demonstrate the control of their function in chemical processes such as catalysis and separation by selecting the optimum structural configuration (Fig. 1).
(Figure 1 caption. A schematic representation of a flexible metal-organic framework, a porous material composed of metal nodes (yellow triangles) interconnected by flexible linkers (blue coils and ribbons). The conformation of the linkers can change depending on the guest molecules present in the pores. Thus the pore shape and chemistry can be chemically controlled to produce a functional material.
To achieve this objective, the project takes a multidisciplinary, experimental and computational, approach that is designed to maximize the understanding of the dynamics of flexible porous materials and to connect these dynamics to their crystal structures and chemical compositions. The project thus aims to establish structure – property – dynamics relationships to guide selection of the chemical components to build flexible porous materials that respond to changes in their environment by single bond rotation, and to enable understanding of the resulting properties. This is required to reveal the possibilities offered by porous materials that change their structures using the mechanisms adopted by biological systems.)
Work performed
The porous materials that are studied in this project belong to the category of metal organic frameworks (MOFs). Their structures consist of a framework of metal centres connected by organic linkers, which defines a porous structure consisting of cavities and channels that are occupied by guest molecules – by control of the interaction between the framework and the guests, we aim to change the structure of the MOF and allow it to perform specific chemical functions. The project targets MOF that can adopt multiple structures and are thus flexible rather than rigid, with the flexibility arising from rotation about the single chemical bonds within the structure of the linker molecule – changes in the structure of the linker molecule due to changes in rotation about single bonds within it are referred to as changes in conformation.
The project integrates experimental work, which involves synthesis, characterisation and property measurement of the new flexible MOFs, with computational work, which involves both the theoretical analysis and understanding of the properties associated with the new flexible MOFs, and the use of this knowledge to guide the design of the next set of MOF to be tackled experimentally by predicting which are the best linkers to choose to access the flexible structures.
The selection of the organic linker is a crucial step for the design of a new flexible MOF because the linker must bring the capability to change its structure by rotating around single bonds and also the chemical functionality that is necessary for the desired application, in particular to allow the interaction with the chemical environment to drive the change in structure. The organic linkers that have been used so far include three classes of molecules (i) pure peptides, (ii) peptide-like molecules that have been designed and synthesized for the purposes of this project and (iii) other commercially available linkers that can change their structures by rotation about single bonds. Each of these classes of molecules has different characteristics relevant to their MOF chemistry, which are their terminal groups that bind to the metal centres to form the solid state crystal structure of the MOF, the number of sp3 carbons (carbons with four other chemically bonded neighbours) that are responsible for the ability to change structure by rotation about single bonds (referred to as conformational flexibility), and the available chemical functionalities.
New MOFs have successfully been synthesized with organic linkers from every class and their crystal structures have been determined by single crystal x-ray diffraction (SCXRD). The structural flexibility of the new MOFs has been explored by exchanging the solvent molecules contained in their pores with a library of small molecules that have been selected using methods from chemical informatics to cover a variety of properties such as polarity, size and functional groups (Fig. 2).
(Figure 2 caption. The structural flexibility of one of the new MOFs, ZnGGH, demonstrated by exchanging the solvent molecules in the pores. Nine distinct structures that differ by linker conformation were identified.
From these exchange experiments, we obtained several crystal structures for each MOF, which were compared to each other. The purpose of these experiments is to understand the range of changes in the MOF features that are responsible for their properties (such as pore size, pore shape, position of functional groups, bonding interactions to the guest molecules in the pores) that can be accessed by changing the chemical species in their pores, ensuring that the full range of possible structures and associated functions are identified.)
The flexible MOFs that have been synthesized to date by the project demonstrate the key features targeted at the outset. Their pore structures and shapes respond dynamically to the guests present within them by chemically-driven rotations about single chemical bonds. This lead
Final results
The team has been able to demonstrate (Nature 565, 2019, 213-217) that chemical control of the exact conformation adopted by a flexible linker through the rotation about its single bonds can trigger a specific chemical function by changing the crystal structure of the MOF, in line with the project aim of controlling chemical properties of flexible porous materials via single bond rotation and guest interaction. This was achieved by the development of the peptide-based crystalline porous material, with the code name ZnGGH, which is able to dynamically adapt its structure in the presence of different guests by reconfiguring the conformation of the flexible peptide chain through rotation about single chemical bonds. ZnGGH adopts nine distinct crystal structures. These structures display different pore sizes, pore geometries and internal surface chemistry because the peptide linker conformations change to give access to these different structures driven by their exact chemical interactions with the guest molecules, all of which were identified by the SCXRD structure determination. These structural changes were understood using the PCA method to analyse the observed linker conformations, which clustered the observed structures into three groups (Fig. 3).
(Figure 3 caption. Dihedral angle principal component analysis (dPCA) of linker conformations observed in 9 experimental structures of ZnGGH. The black circles marked with the number X for each ZnGGH-X structure denote the experimentally observed linker conformations while coloured solid circles correspond to the three pictured linker conformations observed in the calculated empty host structures S-ZnGGH, T-ZnGGH and F-ZnGGH, colour-coded according to their energy per linker. The calculated transition paths between these minima represent the conformational energy landscape of ZnGGH. The solid arrows indicate the positions of energy barriers on the conformational energy landscape and the dashed arrows show the largest change in linker torsions between the calculated structures shown.)
Computational analysis of these three groups revealed they led to three distinct groups of structures that were characteristic of low-energy arrangements of the entire framework. A conformational energy landscape for ZnGGH was constructed using the computationally optimised structures as minima that are connected by the simulated transition pathways. By controlling the structures adopted through the guest molecules selected to interact with the framework, it was possible to produce behaviour in the crystalline porous material that was analogous to both the conformational selection and induced fit modes of guest response that are seen in proteins.
The liquid adsorption properties of the three different groups of ZnGGH structures were tested with dioxane as probe molecule, in order to evaluate how the change in structure driven by chemical bond rotation through guest interaction can change the functional behaviour of a flexible porous material. The structures varied from highly active for dioxane uptake to completely inactive for dioxane uptake, according to their linker conformations. By changing the chemical environment of ZnGGH to transform its structure from an inactive to an active minimum, it was possible to chemically trigger the uptake of the dioxane molecules. The project thus understood the structural transformability of a crystalline porous material in terms of the conformational energy landscape picture used in protein science and controlled the activity of the material for the uptake of a chemical by selecting the appropriate minimum on the landscape by determining the conformation adopted by the linker through interaction with the guests (Fig. 4).
(Figure 4 caption. The demonstration of conformational selection and chemical triggering in ZnGGH: the calculated relative energies per linker are plotted for ZnGGH with DMSO and dioxane in the pores when their positions are optimised in a fl