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Knoll K, Herold D, Hirschmann M, Thiele CM. A supramolecular and liquid crystalline water-based alignment medium based on azobenzene-substituted 1,3,5-benzenetricarboxamides. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2022; 60:563-571. [PMID: 35266585 DOI: 10.1002/mrc.5266] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/04/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
A supramolecular, lyotropic liquid crystalline alignment medium based on an azobenzene-containing 1,3,5-benzenetricarboxamide (BTA) building block is described and investigated. As we demonstrate, this water-based system is suitable for the investigation of various water-soluble analytes and allows for a scaling of alignment strength through variation of temperature. Additionally, alignment is shown to reversibly collapse above a certain temperature, yielding an isotropic solution. This collapse allows for isotropic reference measurements, which are typically needed in addition to those in an anisotropic environment, to be performed using the same sample just by varying the temperature. The medium described thus provides easy access to anisotropic NMR observables and simplifies structure elucidation techniques based thereon.
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Affiliation(s)
- Kevin Knoll
- Clemens-Schöpf-Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Dominik Herold
- Clemens-Schöpf-Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Max Hirschmann
- Clemens-Schöpf-Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
- Department of Fibre and Polymer Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Christina M Thiele
- Clemens-Schöpf-Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
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Koch M, Saphiannikova M, Guskova O. Cyclic Photoisomerization of Azobenzene in Atomistic Simulations: Modeling the Effect of Light on Columnar Aggregates of Azo Stars. Molecules 2021; 26:7674. [PMID: 34946756 PMCID: PMC8709326 DOI: 10.3390/molecules26247674] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/14/2021] [Accepted: 12/15/2021] [Indexed: 12/02/2022] Open
Abstract
This computational study investigates the influence of light on supramolecular aggregates of three-arm azobenzene stars. Every star contains three azobenzene (azo) moieties, each able to undergo reversible photoisomerization. In solution, the azo stars build column-shaped supramolecular aggregates. Previous experimental works report severe morphological changes of these aggregates under UV-Vis light. However, the underlying molecular mechanisms are still debated. Here we aim to elucidate how light affects the structure and stability of the columnar stacks on the molecular scale. The system is investigated using fully atomistic molecular dynamics (MD) simulations. To implement the effects of light, we first developed a stochastic model of the cyclic photoisomerization of azobenzene. This model reproduces the collective photoisomerization kinetics of the azo stars in good agreement with theory and previous experiments. We then apply light of various intensities and wavelengths on an equilibrated columnar stack of azo stars in water. The simulations indicate that the aggregate does not break into separate fragments upon light irradiation. Instead, the stack develops defects in the form of molecular shifts and reorientations and, as a result, it eventually loses its columnar shape. The mechanism and driving forces behind this order-disorder structural transition are clarified based on the simulations. In the end, we provide a new interpretation of the experimentally observed morphological changes.
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Affiliation(s)
- Markus Koch
- Institute Theory of Polymers, Leibniz Institute of Polymer Research Dresden, Hohe Str. 6, 01069 Dresden, Germany;
| | - Marina Saphiannikova
- Institute Theory of Polymers, Leibniz Institute of Polymer Research Dresden, Hohe Str. 6, 01069 Dresden, Germany;
- Dresden Center for Computational Materials Science (DCMS), Technische Universität Dresden, 01062 Dresden, Germany
| | - Olga Guskova
- Institute Theory of Polymers, Leibniz Institute of Polymer Research Dresden, Hohe Str. 6, 01069 Dresden, Germany;
- Dresden Center for Computational Materials Science (DCMS), Technische Universität Dresden, 01062 Dresden, Germany
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Koch M, Saphiannikova M, Guskova O. Columnar Aggregates of Azobenzene Stars: Exploring Intermolecular Interactions, Structure, and Stability in Atomistic Simulations. Molecules 2021; 26:7598. [PMID: 34946680 PMCID: PMC8703797 DOI: 10.3390/molecules26247598] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/09/2021] [Accepted: 12/10/2021] [Indexed: 11/16/2022] Open
Abstract
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 π-π 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 π-π 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, π-π stacking and H-bonds, are required to maintain the columnar arrangement of the aggregates.
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Affiliation(s)
- Markus Koch
- Institute Theory of Polymers, Leibniz Institute of Polymer Research Dresden, Hohe Str. 6, 01069 Dresden, Germany;
| | - Marina Saphiannikova
- Institute Theory of Polymers, Leibniz Institute of Polymer Research Dresden, Hohe Str. 6, 01069 Dresden, Germany;
- Dresden Center for Computational Materials Science (DCMS), Technische Universität Dresden, 01062 Dresden, Germany
| | - Olga Guskova
- Institute Theory of Polymers, Leibniz Institute of Polymer Research Dresden, Hohe Str. 6, 01069 Dresden, Germany;
- Dresden Center for Computational Materials Science (DCMS), Technische Universität Dresden, 01062 Dresden, Germany
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Savchenko V, Koch M, Pavlov AS, Saphiannikova M, Guskova O. Stacks of Azobenzene Stars: Self-Assembly Scenario and Stabilising Forces Quantified in Computer Modelling. Molecules 2019; 24:E4387. [PMID: 31801297 PMCID: PMC6930662 DOI: 10.3390/molecules24234387] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 11/25/2019] [Accepted: 11/28/2019] [Indexed: 12/27/2022] Open
Abstract
In this paper, the columnar supramolecular aggregates of photosensitive star-shaped azobenzenes with benzene-1,3,5-tricarboxamide core and azobenzene arms are analyzed theoretically by applying a combination of computer simulation techniques. Without a light stimulus, the azobenzene arms adopt the trans-state and build one-dimensional columns of stacked molecules during the first stage of the noncovalent association. These columnar aggregates represent the structural elements of more complex experimentally observed morphologies-fibers, spheres, gels, and others. Here, we determine the most favorable mutual orientations of the trans-stars in the stack in terms of (i) the π - π distance between the cores lengthwise the aggregate, (ii) the lateral displacements due to slippage and (iii) the rotation promoting the helical twist and chirality of the aggregate. To this end, we calculate the binding energy diagrams using density functional theory. The model predictions are further compared with available experimental data. The intermolecular forces responsible for the stability of the stacks in crystals are quantified using Hirshfeld surface analysis. Finally, to characterize the self-assembly mechanism of the stars in solution, we calculate the hydrogen bond lengths, the normalized dipole moments and the binding energies as functions of the columnar length. For this, molecular dynamics trajectories are analyzed. Finally, we conclude about the cooperative nature of the self-assembly of star-shaped azobenzenes with benzene-1,3,5-tricarboxamide core in aqueous solution.
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Affiliation(s)
- Vladyslav Savchenko
- Dresden Center for Computational Materials Science (DCMS), Technische Universität Dresden, 01062 Dresden, Germany; (V.S.); (M.S.)
- Institute Theory of Polymers, Leibniz Institute of Polymer Research Dresden, Hohe Str. 6, 01069 Dresden, Germany;
| | - Markus Koch
- Institute Theory of Polymers, Leibniz Institute of Polymer Research Dresden, Hohe Str. 6, 01069 Dresden, Germany;
| | - Aleksander S. Pavlov
- Department of Physical Chemistry, Faculty of Chemistry and Technology, Tver State University, Sadovyj per. 35, Tver 170002, Russia;
| | - Marina Saphiannikova
- Dresden Center for Computational Materials Science (DCMS), Technische Universität Dresden, 01062 Dresden, Germany; (V.S.); (M.S.)
- Institute Theory of Polymers, Leibniz Institute of Polymer Research Dresden, Hohe Str. 6, 01069 Dresden, Germany;
| | - Olga Guskova
- Dresden Center for Computational Materials Science (DCMS), Technische Universität Dresden, 01062 Dresden, Germany; (V.S.); (M.S.)
- Institute Theory of Polymers, Leibniz Institute of Polymer Research Dresden, Hohe Str. 6, 01069 Dresden, Germany;
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Koch M, Saphiannikova M, Guskova O. Do Columns of Azobenzene Stars Disassemble under Light Illumination? LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:14659-14669. [PMID: 31627699 DOI: 10.1021/acs.langmuir.9b02960] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The clustering properties of star-shaped molecules comprising three photochromic azobenzene-containing arms are investigated with specific focus on the influence of light on these structures. Previous experimental works report self-assembly of azobenzene stars in aqueous solution into long columnar clusters that are detectable using optical microscopy. These clusters appear to vanish under UV irradiation, which is known to induce trans-to-cis photoisomerization of the azobenzene groups. We have performed MD simulations, density functional theory, and density functional tight binding calculations to determine conformational properties and binding energies of these clusters. Our simulation data suggest that the binding strength of the clusters is large enough to prevent a breaking along their main axis. We conclude that very likely other mechanisms lead to the apparent disappearance of the clusters.
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Affiliation(s)
- Markus Koch
- Institute Theory of Polymers , Leibniz Institute of Polymer Research Dresden , Hohe Str. 6 , 01069 Dresden , Germany
| | - Marina Saphiannikova
- Institute Theory of Polymers , Leibniz Institute of Polymer Research Dresden , Hohe Str. 6 , 01069 Dresden , Germany
- Dresden Center for Computational Materials Science (DCMS) , Technische Universität Dresden , 01062 Dresden , Germany
| | - Olga Guskova
- Institute Theory of Polymers , Leibniz Institute of Polymer Research Dresden , Hohe Str. 6 , 01069 Dresden , Germany
- Dresden Center for Computational Materials Science (DCMS) , Technische Universität Dresden , 01062 Dresden , Germany
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Castro-Falcón G, Millán-Aguiñaga N, Roullier C, Jensen PR, Hughes CC. Nitrosopyridine Probe To Detect Polyketide Natural Products with Conjugated Alkenes: Discovery of Novodaryamide and Nocarditriene. ACS Chem Biol 2018; 13:3097-3106. [PMID: 30272441 DOI: 10.1021/acschembio.8b00598] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An optimized nitroso-based probe that facilitates the discovery of conjugated alkene-containing natural products in unprocessed extracts was developed. It chemoselectively reacts with conjugated olefins via a nitroso-Diels-Alder cyclization to yield derivatives with a distinct chromophore and an isotopically unique bromine atom that can be rapidly identified using liquid chromatography/mass spectrometry and a bioinformatics tool called MeHaloCoA (Marine Halogenated Compound Analysis). The probe is ideally employed when genome-mining techniques identify strains containing polyketide gene clusters with two or more repeating KS-AT-DH-KR-ACP domain sequences, which are required for the biosynthesis of conjugated alkenes. Comparing the reactivity and spectral properties of five brominated arylnitroso reagents with model compounds spiramycin, bufalin, rapamycin, and rifampicin led to the identification of 5-bromo-2-nitrosopyridine as the most suitable probe structure. The utility of the dienophile probe was then demonstrated in bacterial extracts. Tylactone, novodaryamide and daryamide A, piperazimycin A, and the saccharamonopyrones A and B were cleanly labeled in extracts from their respective bacterial producers, in high regioselectivity but with varying degrees of diastereoselectivity. Further application of the method led to the discovery of a new natural product called nocarditriene, containing an unprecedented epoxy-2,3,4,5-tetrahydropyridine structure, from marine-derived Nocardiopsis strain CNY-503.
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Affiliation(s)
- Gabriel Castro-Falcón
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Natalie Millán-Aguiñaga
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Catherine Roullier
- Mer Molécules Santé - EA2160, Université de Nantes, 44035 Nantes-cedex 1, France
| | - Paul R. Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Chambers C. Hughes
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
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Koch M, Saphiannikova M, Santer S, Guskova O. Photoisomers of Azobenzene Star with a Flat Core: Theoretical Insights into Multiple States from DFT and MD Perspective. J Phys Chem B 2017; 121:8854-8867. [PMID: 28832166 DOI: 10.1021/acs.jpcb.7b07350] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This study focuses on comparing physical properties of photoisomers of an azobenzene star with benzene-1,3,5-tricarboxamide core. Three azobenzene arms of the molecule undergo a reversible trans-cis isomerization upon UV-vis light illumination giving rise to multiple states from the planar all-trans one, via two mixed states to the kinked all-cis isomer. Employing density functional theory, we characterize the structural and photophysical properties of each state indicating a role the planar core plays in the coupling between azobenzene chromophores. To characterize the light-triggered switching of solvophilicity/solvophobicity of the star, the difference in solvation free energy is calculated for the transfer of an azobenzene star from its gas phase to implicit or explicit solvents. For the latter case, classical all-atom molecular dynamics simulations of aqueous solutions of azobenzene star are performed employing the polymer consistent force field to shed light on the thermodynamics of explicit hydration as a function of the isomerization state and on the structuring of water around the star. From the analysis of two contributions to the free energy of hydration, the nonpolar van der Waals and the electrostatic terms, it is concluded that isomerization specificity largely determines the polarity of the molecule and the solute-solvent electrostatic interactions. This convertible hydrophilicity/hydrophobicity together with readjustable occupied volume and the surface area accessible to water, affects the self-assembly/disassembly of the azobenzene star with a flat core triggered by light.
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Affiliation(s)
- Markus Koch
- Institute Theory of Polymers, Leibniz Institute of Polymer Research Dresden , Hohe Str. 6, 01069 Dresden, Germany.,Institute of Theoretical Physics, Technische Universität Dresden , Zellescher Weg 17, 01069 Dresden, Germany
| | - Marina Saphiannikova
- Institute Theory of Polymers, Leibniz Institute of Polymer Research Dresden , Hohe Str. 6, 01069 Dresden, Germany.,Dresden Center for Computational Materials Science (DCMS), Technische Universität Dresden , 01069 Dresden, Germany
| | - Svetlana Santer
- Institute of Physics and Astronomy, University of Potsdam , Karl-Liebknecht-Str. 24/25, 14476 Potsdam, Germany
| | - Olga Guskova
- Institute Theory of Polymers, Leibniz Institute of Polymer Research Dresden , Hohe Str. 6, 01069 Dresden, Germany.,Dresden Center for Computational Materials Science (DCMS), Technische Universität Dresden , 01069 Dresden, Germany
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Kind J, Kaltschnee L, Leyendecker M, Thiele CM. Distinction of trans–cis photoisomers with comparable optical properties in multiple-state photochromic systems – examining a molecule with three azobenzenes via in situ irradiation NMR spectroscopy. Chem Commun (Camb) 2016; 52:12506-12509. [DOI: 10.1039/c6cc06771a] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In situ irradiation NMR spectroscopy allows for the distinction and quantification of different photoisomers.
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Affiliation(s)
- Jonas Kind
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie
- Technische Universität Darmstadt
- D-64287 Darmstadt
- Germany
| | - Lukas Kaltschnee
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie
- Technische Universität Darmstadt
- D-64287 Darmstadt
- Germany
| | - Martin Leyendecker
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie
- Technische Universität Darmstadt
- D-64287 Darmstadt
- Germany
| | - Christina M. Thiele
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie
- Technische Universität Darmstadt
- D-64287 Darmstadt
- Germany
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