Columnar Aggregates of Azobenzene Stars: Exploring Intermolecular Interactions, Structure, and Stability in Atomistic Simulations
We present a simulation study of supramolecular aggregates formed by three-arm azobenzene (Azo) stars with a benzene-1,3,5-tricarboxamide (BTA) core in water. Previous experimental works by other research groups demonstrate that such Azo stars assemble into needle-like structures with light-responsi...
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MDPI AG
2021-12-01
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| Series: | Molecules |
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| Online Access: | https://www.mdpi.com/1420-3049/26/24/7598 |
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| author | Markus Koch Marina Saphiannikova Olga Guskova |
| author_facet | Markus Koch Marina Saphiannikova Olga Guskova |
| author_sort | Markus Koch |
| collection | DOAJ |
| description | We present a simulation study of supramolecular aggregates formed by three-arm azobenzene (Azo) stars with a benzene-1,3,5-tricarboxamide (BTA) core in water. Previous experimental works by other research groups demonstrate that such Azo stars assemble into needle-like structures with light-responsive properties. Disregarding the response to light, we intend to characterize the equilibrium state of this system on the molecular scale. In particular, we aim to develop a thorough understanding of the binding mechanism between the molecules and analyze the structural properties of columnar stacks of Azo stars. Our study employs fully atomistic molecular dynamics (MD) simulations to model pre-assembled aggregates with various sizes and arrangements in water. In our detailed approach, we decompose the binding energies of the aggregates into the contributions due to the different types of non-covalent interactions and the contributions of the functional groups in the Azo stars. Initially, we investigate the origin and strength of the non-covalent interactions within a stacked dimer. Based on these findings, three arrangements of longer columnar stacks are prepared and equilibrated. We confirm that the binding energies of the stacks are mainly composed of <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mi>π</mi></semantics></math></inline-formula>–<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mi>π</mi></semantics></math></inline-formula> interactions between the conjugated parts of the molecules and hydrogen bonds formed between the stacked BTA cores. Our study quantifies the strength of these interactions and shows that the <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mi>π</mi></semantics></math></inline-formula>–<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mi>π</mi></semantics></math></inline-formula> interactions, especially between the Azo moieties, dominate the binding energies. We clarify that hydrogen bonds, which are predominant in BTA stacks, have only secondary energetic contributions in stacks of Azo stars but remain necessary stabilizers. Both types of interactions, <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mi>π</mi></semantics></math></inline-formula>–<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mi>π</mi></semantics></math></inline-formula> stacking and H-bonds, are required to maintain the columnar arrangement of the aggregates. |
| first_indexed | 2024-03-10T03:28:46Z |
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| language | English |
| last_indexed | 2024-03-10T03:28:46Z |
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| spelling | doaj.art-db9fd8f190a74a57a294dec7a9288a342023-11-23T09:46:31ZengMDPI AGMolecules1420-30492021-12-012624759810.3390/molecules26247598Columnar Aggregates of Azobenzene Stars: Exploring Intermolecular Interactions, Structure, and Stability in Atomistic SimulationsMarkus Koch0Marina Saphiannikova1Olga Guskova2Institute Theory of Polymers, Leibniz Institute of Polymer Research Dresden, Hohe Str. 6, 01069 Dresden, GermanyInstitute Theory of Polymers, Leibniz Institute of Polymer Research Dresden, Hohe Str. 6, 01069 Dresden, GermanyInstitute Theory of Polymers, Leibniz Institute of Polymer Research Dresden, Hohe Str. 6, 01069 Dresden, GermanyWe present a simulation study of supramolecular aggregates formed by three-arm azobenzene (Azo) stars with a benzene-1,3,5-tricarboxamide (BTA) core in water. Previous experimental works by other research groups demonstrate that such Azo stars assemble into needle-like structures with light-responsive properties. Disregarding the response to light, we intend to characterize the equilibrium state of this system on the molecular scale. In particular, we aim to develop a thorough understanding of the binding mechanism between the molecules and analyze the structural properties of columnar stacks of Azo stars. Our study employs fully atomistic molecular dynamics (MD) simulations to model pre-assembled aggregates with various sizes and arrangements in water. In our detailed approach, we decompose the binding energies of the aggregates into the contributions due to the different types of non-covalent interactions and the contributions of the functional groups in the Azo stars. Initially, we investigate the origin and strength of the non-covalent interactions within a stacked dimer. Based on these findings, three arrangements of longer columnar stacks are prepared and equilibrated. We confirm that the binding energies of the stacks are mainly composed of <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mi>π</mi></semantics></math></inline-formula>–<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mi>π</mi></semantics></math></inline-formula> interactions between the conjugated parts of the molecules and hydrogen bonds formed between the stacked BTA cores. Our study quantifies the strength of these interactions and shows that the <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mi>π</mi></semantics></math></inline-formula>–<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mi>π</mi></semantics></math></inline-formula> interactions, especially between the Azo moieties, dominate the binding energies. We clarify that hydrogen bonds, which are predominant in BTA stacks, have only secondary energetic contributions in stacks of Azo stars but remain necessary stabilizers. Both types of interactions, <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mi>π</mi></semantics></math></inline-formula>–<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mi>π</mi></semantics></math></inline-formula> stacking and H-bonds, are required to maintain the columnar arrangement of the aggregates.https://www.mdpi.com/1420-3049/26/24/7598azobenzenessupramolecular assemblyhydrogen bondingmolecular dynamicscomputer simulations |
| spellingShingle | Markus Koch Marina Saphiannikova Olga Guskova Columnar Aggregates of Azobenzene Stars: Exploring Intermolecular Interactions, Structure, and Stability in Atomistic Simulations Molecules azobenzenes supramolecular assembly hydrogen bonding molecular dynamics computer simulations |
| title | Columnar Aggregates of Azobenzene Stars: Exploring Intermolecular Interactions, Structure, and Stability in Atomistic Simulations |
| title_full | Columnar Aggregates of Azobenzene Stars: Exploring Intermolecular Interactions, Structure, and Stability in Atomistic Simulations |
| title_fullStr | Columnar Aggregates of Azobenzene Stars: Exploring Intermolecular Interactions, Structure, and Stability in Atomistic Simulations |
| title_full_unstemmed | Columnar Aggregates of Azobenzene Stars: Exploring Intermolecular Interactions, Structure, and Stability in Atomistic Simulations |
| title_short | Columnar Aggregates of Azobenzene Stars: Exploring Intermolecular Interactions, Structure, and Stability in Atomistic Simulations |
| title_sort | columnar aggregates of azobenzene stars exploring intermolecular interactions structure and stability in atomistic simulations |
| topic | azobenzenes supramolecular assembly hydrogen bonding molecular dynamics computer simulations |
| url | https://www.mdpi.com/1420-3049/26/24/7598 |
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