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-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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Cyclic Photoisomerization of Azobenzene in Atomistic Simulations: Modeling the Effect of Light on Columnar Aggregates of Azo Stars

Molecules ◽

10.3390/molecules26247674 ◽

2021 ◽

Vol 26 (24) ◽

pp. 7674

Author(s):

Markus Koch ◽

Marina Saphiannikova ◽

Olga Guskova

Keyword(s):

Molecular Mechanisms ◽

Driving Forces ◽

Computational Study ◽

Morphological Changes ◽

Md Simulations ◽

Atomistic Simulations ◽

Experimental Works ◽

New Interpretation ◽

Kinetics Of ◽

Supramolecular Aggregates

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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Phenazine derivatives for optical sensing: a review

Journal of Materials Chemistry C ◽

10.1039/d0tc01401j ◽

2020 ◽

Vol 8 (33) ◽

pp. 11308-11339 ◽

Cited By ~ 1

Author(s):

Qi Xiao-Ni ◽

Li-Rong Dang ◽

Wen-Jun Qu ◽

You-Ming Zhang ◽

Hong Yao ◽

...

Keyword(s):

Hydrogen Bonds ◽

Optical Sensing ◽

Lone Pair ◽

Metal Coordination ◽

Optical Performance ◽

Π Interactions ◽

Non Covalent Interactions ◽

Weak Forces ◽

Covalent Interactions

Phenazine exhibiting an electron-deficient skeleton, lone pair of electrons on nitrogen atoms, and other properties (such as tunable structures, excellent optical performance and proper binding abilities) can effectively sense target ions or molecules via non-covalent interactions, involving hydrogen bonds, anion–π interactions, metal coordination and other weak forces.

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Role of non-covalent interactions in the supramolecular architectures of mercury(ii) diphenyldithiophosphates: An experimental and theoretical investigation

New Journal of Chemistry ◽

10.1039/d0nj05709f ◽

2021 ◽

Vol 45 (4) ◽

pp. 2249-2263

Author(s):

Pretam Kumar ◽

Snehasis Banerjee ◽

Anu Radha ◽

Tahira Firdoos ◽

Subash Chandra Sahoo ◽

...

Keyword(s):

Theoretical Investigation ◽

Supramolecular Organization ◽

Π Interactions ◽

Supramolecular Architectures ◽

Non Covalent Interactions ◽

Covalent Interactions

The H-bond, spodium bond and CH⋯π interactions playing an important role in the supramolecular organization of two mercury(ii) diphenyldithiophosphate complexes have been discussed.

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Resolving the Dynamic Non-Covalent Interaction inside Membrane Protein Channel by Single-Molecule Interaction Spectrum

10.26434/chemrxiv.7251683 ◽

2018 ◽

Author(s):

Meng-Yin Li ◽

Yi-Lun Ying ◽

Xi-Xin Fu ◽

Jie Yu ◽

Shao-Chuang Liu ◽

...

Keyword(s):

Membrane Protein ◽

Single Molecule ◽

Ionic Current ◽

Md Simulations ◽

Energy Spectra ◽

Membrane Channels ◽

Non Covalent Interactions ◽

Protein Channels ◽

Covalent Interactions ◽

Molecule Interaction

Millions of years of evolution have produced membrane protein channels capable of efficiently moving ions across the cell membrane. The underlying fundamental mechanisms that facilitate these actions greatly contribute to the weak non-covalent interactions. However, uncovering these dynamic interactions and its synergic network effects still remains challenging in both experimental techniques and molecule dynamics (MD) simulations. Here, we present a rational strategy that combines MD simulations and frequency-energy spectroscopy to identify and quantify the role of non-covalent interactions in carrier transport through membrane protein channels, as encoded in traditional single channel recording or ionic current. We employed wild-type aerolysin transporting of methylcytosine and cytosine as a model to explore the dynamic ionic signatures with non-stationary and non-linear frequency analysis. Our data illuminate that methylcytosine experiences strong non-covalent interactions with the aerolysin nanopore at Region 1 around R220 than cytosine, which produces characteristic frequency-energy spectra. Furthermore, we experimentally validate the obtained hypothesis from frequency-energy spectra by designing single-site mutation of K238G which creates significantly enhanced non-covalent interactions for the recognition of methylcytosine. The frequency-energy spectrum of ions flowing inside membrane channels constitutes a single-molecule interaction spectrum, which bridges the gap between traditional ionic current recording and the MD simulations, facilitating the qualitative and quantitive description of the non-covalent interactions inside membrane channels.

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New approaches to organocatalysis based on C–H and C–X bonding for electrophilic substrate activation

Beilstein Journal of Organic Chemistry ◽

10.3762/bjoc.12.283 ◽

2016 ◽

Vol 12 ◽

pp. 2834-2848 ◽

Cited By ~ 33

Author(s):

Pavel Nagorny ◽

Zhankui Sun

Keyword(s):

Hydrogen Bond ◽

Hydrogen Bonds ◽

Recent Progress ◽

Halogen Bonds ◽

Hydrogen Bond Donor ◽

New Approaches ◽

Substrate Activation ◽

Non Covalent Interactions ◽

Covalent Interactions ◽

Hydrogen Bond Donors

Hydrogen bond donor catalysis represents a rapidly growing subfield of organocatalysis. While traditional hydrogen bond donors containing N–H and O–H moieties have been effectively used for electrophile activation, activation based on other types of non-covalent interactions is less common. This mini review highlights recent progress in developing and exploring new organic catalysts for electrophile activation through the formation of C–H hydrogen bonds and C–X halogen bonds.

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Covalent and non-covalent interactions of cyanidin-3-O-glucoside with milk proteins revealed modifications in protein conformational structures, digestibility, and allergenic characteristics

Food & Function ◽

10.1039/d1fo01946e ◽

2021 ◽

Author(s):

Qiaozhi Zhang ◽

Zhouzhou Cheng ◽

Ruyan Chen ◽

Yanbo Wang ◽

Song Miao ◽

...

Keyword(s):

Milk Proteins ◽

Different Types ◽

Non Covalent Interactions ◽

Covalent Interactions

Currently, there is a need to explore the consequences of different types of protein-anthocyanin complexations, as well as possible changes in the nutrition and allergenicity of formed complexes. Here, we...

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The Importance of CH···X (X = O, π) Interaction of a New Mixed Ligand Cu(II) Coordination Polymer: Structure, Hirshfeld Surface and Theoretical Studies

Crystals ◽

10.3390/cryst8120455 ◽

2018 ◽

Vol 8 (12) ◽

pp. 455 ◽

Cited By ~ 16

Author(s):

Saikat Seth

Keyword(s):

Solid State ◽

Hydrogen Bonds ◽

Noncovalent Interactions ◽

Carbonyl Oxygen ◽

Hirshfeld Surface ◽

Mixed Ligand ◽

Binding Energies ◽

Zigzag Chain ◽

X Ray ◽

Π Interactions

In this study, a new equimolar (1:1:1) mixed ligand Cu(II) polymer, [Cu(IDA)(ImP)]n (1) with iminodiacetato (IDA) and imidazo[1,2-a]-pyridine (ImP) was synthesized and characterized by single crystal X-ray diffraction analysis. X-ray crystallography reveals that compound (1) consists of polymeric zigzag chain along [010] the carboxylate carbonyl oxygen atom by two-fold symmetry screw axis. The solid-state structure is stabilized through C–H···O hydrogen bonds and C–H···π interactions that lead the molecules to generate two-dimensional supramolecular assemblies. The intricate combinations of hydrogen bonds and C–H···π interactions are fully described along with computational studies. A thorough analysis of Hirshfeld surface and fingerprint plots elegantly quantify the interactions involved within the structure. The binding energies associated with the noncovalent interactions observed in the crystal structure and the interplay between them were calculated using theoretical DFT calculations. Weak noncovalent interactions were analyzed and characterized using Bader’s theory of ‘‘atoms-in-molecules’’ (AIM). Finally, the solid-state supramolecular assembly was characterized by the “Noncovalent Interaction” (NCI) plot index.

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Studying physisorption processes and molecular friction of cycloparaphenylene molecules on graphene nano-sized flakes: role of π⋯π and CH⋯π interactions

Molecular Systems Design & Engineering ◽

10.1039/c7me00024c ◽

2017 ◽

Vol 2 (3) ◽

pp. 253-262 ◽

Cited By ~ 3

Author(s):

A. Pérez-Guardiola ◽

A. J. Pérez-Jiménez ◽

J. C. Sancho-García

Keyword(s):

Cost Effective ◽

Π Interactions ◽

Graphene Flakes ◽

Non Covalent Interactions ◽

Molecular Friction ◽

Covalent Interactions

We theoretically study, by means of dispersion-corrected and cost-effective methods, the strength of non-covalent interactions between cyclic organic nanorings and nano-sized graphene flakes acting as substrates.

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