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Ganna (Anya) Gryn'ova

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Date Published: 1st Aug 2023

Publication Type: Journal

Matrix of orthogonalized atomic orbital coefficients representation for radicals and ions

Abstract (Expand)

Chemical (molecular, quantum) machine learning relies on representing molecules in unique and informative ways. Here, we present the matrix of orthogonalized atomic orbital coefficients (MAOC) as a … quantum-inspired molecular and atomic representation containing both structural (composition and geometry) and electronic (charge and spin multiplicity) information. MAOC is based on a cost-effective localization scheme that represents localized orbitals via a predefined set of atomic orbitals. The latter can be constructed from such small atom-centered basis sets as pcseg-0 and STO-3G in conjunction with guess (non-optimized) electronic configuration of the molecule. Importantly, MAOC is suitable for representing monatomic, molecular, and periodic systems and can distinguish compounds with identical compositions and geometries but distinct charges and spin multiplicities. Using principal component analysis, we constructed a more compact but equally powerful version of MAOC—PCX-MAOC. To test the performance of full and reduced MAOC and several other representations (CM, SOAP, SLATM, and SPAHM), we used a kernel ridge regression machine learning model to predict frontier molecular orbital energy levels and ground state single-point energies for chemically diverse neutral and charged, closed- and open-shell molecules from an extended QM7b dataset, as well as two new datasets, N-HPC-1 (N-heteropolycycles) and REDOX (nitroxyl and phenoxyl radicals, carbonyl, and cyano compounds). MAOC affords accuracy that is either similar or superior to other representations for a range of chemical properties and systems.

Authors: Stiv Llenga, Ganna Gryn’ova

Date Published: 7th Jun 2023

Publication Type: Journal

Engineering Host–Guest Interactions in Organic Framework Materials for Drug Delivery

Abstract (Expand)

Metal-organic frameworks (MOF) and covalent organic frameworks (COFs) are promising nanocarriers for targeted drug delivery. Noncovalent interactions between frameworks and drugs play a fundamental … role in the therapeutic uptake and release of the latter. However, the scope of framework functionalizations and deliverable drugs remains underexplored. Using a multilevel approach combining molecular docking and density functional theory, we show for a range of drugs and frameworks that experimentally reported release metrics are in good agreement with the in silico computed host–guest interaction energies. Functional groups within the framework significantly impact the strength of these host–guest interactions, while a given framework can serve as an efficient delivery agent for drugs beyond the prototypical few. Our findings identify the interaction energy as a reliable and relatively easy to compute descriptor of organic framework materials for drug delivery, able to facilitate their high-throughput screening and targeted design towards extended-release times.

Authors: Michelle Ernst, Ganna Gryn'ova

Date Published: 26th May 2023

Publication Type: Journal

Collagen breaks at weak sacrificial bonds taming its mechanoradicals

Abstract (Expand)

Collagen is a force-bearing, hierarchical structural protein important to all connective tissue. In tendon collagen, high load even below macroscopic failure level creates mechanoradicals by homolytic … bond scission, similar to polymers. The location and type of initial rupture sites critically decide on both the mechanical and chemical impact of these micro-ruptures on the tissue, but are yet to be explored. We here use scale-bridging simulations supported by gel electrophoresis and mass spectrometry to determine breakage points in collagen. We find collagen crosslinks, as opposed to the backbone, to harbor the weakest bonds, with one particular bond in trivalent crosslinks as the most dominant rupture site. We identify this bond as sacrificial, rupturing prior to other bonds while maintaining the material’s integrity. Also, collagen’s weak bonds funnel ruptures such that the potentially harmful mechanoradicals are readily stabilized. Our results suggest this unique failure mode of collagen to be tailored towards combatting an early onset of macroscopic failure and material ageing.

Authors: Benedikt Rennekamp, Christoph Karfusehr, Markus Kurth, Aysecan Ünal, Kai Riedmiller, Ganna Gryn’ova, David M. Hudson, Frauke Gräter

Date Published: 12th Apr 2023

Publication Type: Journal

Experimental and Computational Study on the Effects of High Pressure on the Crystal Structure of Boron Nitrilotriacetate

Abstract (Expand)

Herein, we report the structural changes occurring to the molecule of boron nitrilotriacetate and its interactions when the crystal is under compression. A special focus is on the intermolecular … interactions involving the carbonyl groups. In fact, these short-range contacts may anticipate cooperative addition reactions that could eventually lead to a polymer. However, X-ray diffraction experiments do not evidence any polymerization at least up to 16 GPa, due to competing interactions. In this work, we use and illustrate several theoretical tools to investigate the variable nature of the intermolecular interactions and their changes upon compression.

Authors: Fabio Montisci, Michelle Ernst, Piero Macchi

Date Published: 5th Apr 2023

Publication Type: Journal

Metal-Free Molecular Catalysts for the Oxygen Reduction Reaction: Electron Affinity as an Activity Descriptor

Abstract (Expand)

Heteroatom-doped polyaromatic hydrocarbons (or nanographenes) are promising molecular electrocatalysts for the oxygen reduction reaction (ORR). Here, we use density functional theory to investigate the … first step of the ORR pathway (chemisorption) for a set of molecules with experimentally determined catalytic activities. Weak chemisorption is found for only negatively charged catalysts, and a strong correlation is observed between the computed electron affinities and experimental catalytic activities for a range of B- and B,N-doped polyaromatic hydrocarbons. The electron affinity is put forward as a simple activity descriptor of charged (activated) catalysts on an electrode.

Authors: Christopher Ehlert, Anna Piras, Juliette Schleicher, Ganna Gryn’ova

Date Published: 19th Jan 2023

Publication Type: Journal

Locating Guest Molecules inside Metal–Organic Framework Pores with a Multilevel Computational Approach

Abstract (Expand)

Molecular docking has traditionally mostly been employed in the field of protein–ligand binding. Here, we extend this method, in combination with DFT-level geometry optimizations, to locate guest … molecules inside the pores of metal–organic frameworks. The position and nature of the guest molecules tune the physicochemical properties of the host–guest systems. Therefore, it is essential to be able to reliably locate them to rationally enhance the performance of the known metal–organic frameworks and facilitate new material discovery. The results obtained with this approach are compared to experimental data. We show that the presented method can, in general, accurately locate adsorption sites and structures of the host–guest complexes. We therefore propose our approach as a computational alternative when no experimental structures of guest-loaded MOFs are available. Additional information on the adsorption strength in the studied host–guest systems emerges from the computed interaction energies. Our findings provide the basis for other computational studies on MOF–guest systems and contribute to a better understanding of the structure–interaction–property interplay associated with them.

Authors: Michelle Ernst, Tomasz Poręba, Lars Gnägi, Ganna Gryn’ova

Date Published: 12th Jan 2023

Publication Type: Journal

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