Self‐Assembling Behaviour of Perylene, Perylene Diimide, and Thionated Perylene Diimide Deciphered through Non‐Covalent Interactions

Parida, Sanjukta; Patra, Sanjib K.; Mishra, Sabyashachi

doi:10.1002/cphc.202200361

Cited by 16 publications

(12 citation statements)

References 102 publications

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“…3 cluster, we calculated an absolute cooperativity of −6.52 kcal/mol and −6.9 kcal/ mol using the ωB97X-D/aug-cc-pVDZ level of theory and the AMOEBA force field, respectively. For NH (H O) 3 2…”

Section: ■ Results and Discussionmentioning

confidence: 99%

“…Cooperativity plays a crucial role in understanding various biological processes, including molecular recognition, homochirality, protein folding, and self-assembly. − Cooperativity refers to the nonadditive and synergistic effects that arise when multiple components interact, leading to enhanced stability or activity. One of the most well-known examples of cooperativity is the binding of aqueous O 2 to hemoglobin.…”

Section: Introductionmentioning

confidence: 99%

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Cooperativity and Frustration Effects (or Lack Thereof) in Polarizable and Non-polarizable Force Fields

Nochebuena,

Piquemal,

Liu

et al. 2023

J. Chem. Theory Comput.

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Understanding cooperativity and frustration is crucial for studying biological processes such as molecular recognition and protein aggregation. Force fields have been extensively utilized to explore cooperativity in the formation of protein secondary structures and self-assembled systems. Multiple studies have demonstrated that polarizable force fields provide more accurate descriptions of this phenomenon compared to fixed-charge pairwise nonpolarizable force fields, thanks to the incorporation of polarization effects. In this study, we assess the performance of the AMOEBA polarizable force field and the AMBER and OPLS nonpolarizable pairwise force fields in capturing positive and negative cooperativity recently explored in neutral and charged molecular clusters using density functional theory. Our findings show that polarizable and nonpolarizable force fields qualitatively reproduce the relative cooperativity observed in electron structure calculations. However, AMBER and OPLS fail to describe absolute cooperativity. In contrast, AMOEBA accounts for the absolute cooperativity by considering interactions beyond pairwise interactions. According to the energy decomposition analysis, it is observed that the electrostatic interactions calculated with the AMBER and OPLS force fields seem to play an important and counterintuitive role in reproducing the adiabatic interaction energies calculated with density functional theory. However, it is important to note that these force fields, due to their nature, do not explicitly incorporate many-body effects, which limits their ability to accurately describe cooperativity. On the other hand, frustration in polarizable and nonpolarizable force fields is caused by changes in bond stretching and angle bending terms of the building blocks when they are forming a complex.

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Section: ■ Results and Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Cooperativity and Frustration Effects (or Lack Thereof) in Polarizable and Non-polarizable Force Fields

Nochebuena,

Piquemal,

Liu

et al. 2023

J. Chem. Theory Comput.

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show abstract

“…Moreover, Oyspenko et al published a "hot paper" in 2019 for their advances in the thermal control over the self-assembly of TTA supramolecular helical organogels that further stack into larger fibers [82]. More recently, Parida et al [83] exploited the stabilizing interactions occurring in the supramolecular assemblies of a family of perylene-based polymers. In this context, perylene-bisimides (PBIs) had been previously reported to exhibit potent biological applications since they form stable self-assemblies in aqueous media [84].…”

Section: Supramolecular Self-assembly: From Single To Complex Well-or...mentioning

confidence: 99%

Responsive Supramolecular Polymers for Diagnosis and Treatment

Martínez-Orts,

Pujals

2024

IJMS

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Stimuli-responsive supramolecular polymers are ordered nanosized materials that are held together by non-covalent interactions (hydrogen-bonding, metal-ligand coordination, π-stacking and, host–guest interactions) and can reversibly undergo self-assembly. Their non-covalent nature endows supramolecular polymers with the ability to respond to external stimuli (temperature, light, ultrasound, electric/magnetic field) or environmental changes (temperature, pH, redox potential, enzyme activity), making them attractive candidates for a variety of biomedical applications. To date, supramolecular research has largely evolved in the development of smart water-soluble self-assemblies with the aim of mimicking the biological function of natural supramolecular systems. Indeed, there is a wide variety of synthetic biomaterials formulated with responsiveness to control and trigger, or not to trigger, aqueous self-assembly. The design of responsive supramolecular polymers ranges from the use of hydrophobic cores (i.e., benzene-1,3,5-tricarboxamide) to the introduction of macrocyclic hosts (i.e., cyclodextrins). In this review, we summarize the most relevant advances achieved in the design of stimuli-responsive supramolecular systems used to control transport and release of both diagnosis agents and therapeutic drugs in order to prevent, diagnose, and treat human diseases.

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“…27 By exploring the non-covalent interactions to understand self-assembly, a parallel step-wise H-type aggregation pattern was observed in the oligomers of perylene, PDI, and thionated PDI. 28 Despite PDI forming different aggregate systems depending on substituents at the imide and bay positions, twisted core, H-bonding, etc. , 26 the driving force within the PDI structure for self-assembly into H-, J-, X-, M-, and (+)-aggregates remains elusive.…”

Section: Introductionmentioning

confidence: 99%