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publications
S. Kotha, M. F. J. Mabesoone, D. Srideep, R. Sahu, S. K. Reddy, K. V. Rao, Supramolecular depolymerization in the mixture of two poor solvents: mechanistic insights and modulation of supramolecular polymerization of ionic π‐Systems. Angewandte Chemie 133, 5519–5526 (2020).
Published in , 1900
Solvents are fundamentally essential for the synthesis and processing of soft materials. Supramolecular polymers (SPs), an emerging class of soft materials, are usually stable in single and mixtures of poor solvents. In contrast to these preconceived notions, here we report the depolymerization of SPs in the mixture of two poor solvents. This surprising behavior was observed for well-known cationic perylene diimides (cPDIs) in the mixtures of water and amphiphilic organic solvents such as isopropanol (IPA). cPDIs form stable SPs in water and IPA but readily depolymerize into monomers in 50–70 vol% IPA containing water. This is due to the selective solvation of the π-surface of cPDIs by alkyl chains of IPA and ionic side chains by water, as evidenced by molecular dynamic simulations. Moreover, by systematically changing the ratio between water and amphiphilic organic solvent, we could achieve an unprecedented supramolecular polymerization both by increasing and decreasing the solvent polarity.
R. Sahu, S. S. R. K. C. Yamijala, K. V. Rao, S. K. Reddy, Dispersion‐Driven Cooperativity in Alkyl Perylene Diimide Oligomers: Insights from Density Functional Theory. ChemPhysChem 25 (2024).
Published in , 1900
The cooperative mechanism is of paramount importance in the synthesis of supramolecular polymers with desired characteristics, including molecular mass, polydispersity, and morphology. It is primarily driven by the presence of intermolecular interactions, which encompass strong hydrogen bonding, metal-ligand interactions, and dipole-dipole interactions. In this study, we utilize density functional theory and energy decomposition analysis to investigate the cooperative behavior of perylene diimide (PDI) oligomers with alkyl chains at their imide positions, which lack the previously mentioned interactions. Our systematic examination reveals that dispersion interactions originating from the alkyl side-chain substituents play an important role in promoting cooperativity within these PDIs. This influence becomes even more pronounced for alkyl chain lengths beyond hexyl groups. The energy decomposition analysis reveals that the delicate balance between dispersion energy and Pauli repulsion energy is the key driver of cooperative behavior in PDIs. Additionally, we have developed a mathematical model capable of predicting the saturated binding energies for PDI oligomers of varying sizes and alkyl chain lengths. Overall, our findings emphasize the previously undervalued significance of dispersion forces in cooperative supramolecular polymerization, enhancing our overall understanding of the cooperative mechanism.
S. H. Goudar, D. S. Ingle, R. Sahu, S. Kotha, S. K. Reddy, D. J. Babu, K. V. Rao, Perylene Diimide-Containing dynamic hyper-crosslinked ionic porous organic polymers: modulation of assembly and gas storage. ACS Applied Polymer Materials 5, 2097–2104 (2023).
Published in , 1900
A strategy to synthesize hyper-crosslinked polymers with strong visible-light absorption and abundant ionic sites is discussed. This is achieved in a one-pot reaction via the simultaneous Friedel–Crafts alkylation and quaternization reaction between α,α′-dibromo-p-xylene (DBX) and perylene diimide (PDI) substituted with N,N-dimethyl ethylene to result in hyper-crosslinked ionic polymers (HIPs). These HIPs display good surface areas with strong visible-light absorption (400–650 nm) and dispersibility in polar solvents like water and DMSO. Importantly, our experimental and theoretical studies indicate that PDI-HIPs possess a dynamic network with good uptake of water up to seven times their weight. Notably, PDI in PDI-HIPs is not only responsible for visible-light absorption but also acts as a probe to study their dynamic nature. Moreover, the presence of ultramicropores and CO2-philic functional groups in PDI-HIPs renders good CO2 uptake up to 2.11 mmol/g at 273 K despite their relatively low surface area.
S. Kotha†, R. Sahu†, D. Srideep, S. S. R. K. C. Yamijala, S. K. Reddy, K. V. Rao, Cooperative supramolecular polymerization guided by dispersive interactions. Chemistry - an Asian Journal 17 (2022). († = Equal contribution)
Published in , 1900
Cooperative supramolecular polymerization is important for the synthesis of functional supramolecular homo and block-copolymers of π-systems. Current strategies indicate the need of strong hydrogen bonding (H-bonding) and/or dipolar interactions in the π-systems to achieve cooperativity. In sharp contrast, here we report the cooperative supramolecular polymerization in alkyl chain substituted perylene diimides (alkyl PDIs) driven by dispersive interactions with molecular level understanding. Moreover, alkyl PDIs follow cooperative mechanism with cooperativity similar to the strong H-bonded π-systems (σ ∼10−5) despite the lack of strong H-bonding and dipolar interactions. Computer simulations show that this surprising phenomenon in alkyl PDIs is driven by the efficient dispersive interactions among the alkyl chains and π-cores due to their zigzag arrangement in the supramolecular polymer. Importantly, alkyl PDIs display cooperative supramolecular polymerization in both polar and non-polar solvents which is difficult for H-bonded/dipolar π-systems thus highlighting the advantages of dispersive interactions.
S. Kotha, R. Sahu, A. C. Yadav, P. Sharma, B. V. V. S. P. Kumar, S. K. Reddy, K. V. Rao, Noncovalent synthesis of homo and hetero-architectures of supramolecular polymers via secondary nucleation. Nature Communications 15 (2024).
Published in , 1900
The synthesis of supramolecular polymers with controlled architecture is a grand challenge in supramolecular chemistry. Although living supramolecular polymerization via primary nucleation has been extensively studied for controlling the supramolecular polymerization of small molecules, the resulting supramolecular polymers have typically exhibited one-dimensional morphology. In this report, we present the synthesis of intriguing supramolecular polymer architectures through a secondary nucleation event, a mechanism well-established in protein aggregation and the crystallization of small molecules. To achieve this, we choose perylene diimide with 2-ethylhexyl chains at the imide position as they are capable of forming dormant monomers in solution. Activating these dormant monomers via mechanical stimuli and hetero-seeding using propoxyethyl perylene diimide seeds, secondary nucleation event takes over, leading to the formation of three-dimensional spherical spherulites and scarf-like supramolecular polymer heterostructures, respectively. Therefore, the results presented in this study propose a simple molecular design for synthesizing well-defined supramolecular polymer architectures via secondary nucleation.
R. Sahu, D. Nayar, Crowding effects on water-mediated hydrophobic interactions. The Journal of Chemical Physics 155 (2021).
Published in , 1900
Understanding the fundamental forces such as hydrophobic interactions in a crowded intracellular environment is necessary to comprehensively decipher the mechanisms of protein folding and biomolecular self-assemblies. The widely accepted entropic depletion view of crowding effects primarily attributes biomolecular compaction to the solvent excluded volume effects exerted by the “inert” crowders, neglecting their soft interactions with the biomolecule. In this study, we examine the effects of chemical nature and soft attractive energy of crowders on the water-mediated hydrophobic interaction between two non-polar neopentane solutes using molecular dynamics simulations. The crowded environment is modeled using dipeptides composed of polar and non-polar amino acids of varying sizes. The results show that amongst the non-polar crowders, Leu2 strengthens the hydrophobic interactions significantly, whereas the polar and small-sized non-polar crowders do not show significant strengthening. Distinct underlying thermodynamic driving forces are illustrated where the small-sized crowders drive hydrophobic interaction via a classic entropic depletion effect and the bulky crowders strengthen it by preferential interaction with the solute. A crossover from energy-stabilized solvent-separated pair to entropy-stabilized contact pair state is observed in the case of bulky non-polar (Leu2) and polar (Lys2) crowders. The influence of solute–crowder energy in affecting the dehydration energy penalty is found to be crucial for determining the neopentane association. The findings demonstrate that along with the entropic (size) effects, the energetic effects also play a crucial role in determining hydrophobic association. The results can be extended and have implications in understanding the impact of protein crowding with varying chemistry in modulating the protein free energy landscapes.
S. Kotha†, R. Sahu†, A. C. Yadav, K. K. Bejagam, S. K. Reddy, K. V. Rao, Pathway Selection in Temporal Evolution of Supramolecular Polymers of Ionic π‐systems: Amphiphilic Organic Solvent Dictates the Fate of Water. Chemistry - a European Journal 30 (2024). († = Equal contribution)
Published in , 1900
Understanding solvent-solute interactions is essential to designing and synthesising soft materials with tailor-made functions. Although the interaction of the solute with the solvent mixture is more complex than the single solvent medium, solvent mixtures are exciting to unfold several unforeseen phenomena in supramolecular chemistry. Here, we report two unforeseen pathways observed during the hierarchical assembly of cationic perylene diimides (cPDIs) in water and amphiphilic organic solvent (AOS) mixtures. When the aqueous supramolecular polymers (SPs) of cPDIs are injected into AOS, initially kinetically trapped short SPs are formed, which gradually transform into thermodynamically stable high aspect ratio SP networks. Using various experimental and theoretical investigations, we found that this temporal evolution follows two distinct pathways depending on the nature of the water-AOS interactions. If the AOS is isopropanol (IPA), water is released from cPDIs into bulk IPA due to strong hydrogen bonding interactions, which further decreases the monomer concentration of cPDIs (Pathway-1). In the case of dioxane AOS, cPDI monomer concentration further increases as water is retained among cPDIs (Pathway-2) due to relatively weak interactions between dioxane and water. Interestingly, these two pathways are accelerated by external stimuli such as heat and mechanical agitation.
S. Panigrahy†, R. Sahu†, S. K. Reddy, D. Nayar, Structure, energetics and dynamics in crowded amino acid solutions: a molecular dynamics study. Physical Chemistry Chemical Physics 25, 5430–5442 (2023). († = Equal contribution)
Published in , 1900
A comprehensive understanding of crowding effects on biomolecular processes necessitates investigating the bulk thermodynamic and kinetic properties of the solutions with an accurate molecular representation of the crowded milieu. Recent studies have reparameterized the non-bonded dispersion interaction of solutes to precisely model intermolecular interactions, which would circumvent artificial aggregation as shown by the original force-fields. However, the performance of this reparameterization is yet to be assessed for concentrated crowded solutions in terms of investigating the hydration shell structure, energetics and dynamics. In this study, we perform molecular dynamics simulations of crowded aqueous solutions of five zwitterionic neutral amino acids (Gly, Ala, Thr, Pro, and Ser), mimicking the molecular crowding environment, using a modified AMBER ff99SB-ILDN force-field. We systematically examine and show that the reproducibility of the osmotic coefficients, density, viscosity and self-diffusivity of amino acids improves using the modified force-field in crowded concentrations. The modified force-field also improves the structuring of the solute solvation shells, solute interaction energy and convergence of tails of radial distribution functions, indicating reduction in the artificial aggregation. Our results also indicate that the hydrogen bonding network of water weakens and water molecules anomalously diffuse at small time scales in the crowded solutions. These results underscore the significance of examining the solution properties and anomalous hydration behaviour of water in crowded solutions, which have implications in shaping the structure and dynamics of biomolecules. The findings also illustrate the improvement in predicting bulk solution properties using the modified force-field, thereby providing an approach towards accurate modeling of crowded molecular solutions.
A. Ghosh, R. Sahu, S. K. Reddy, Constructing one-dimensional supramolecular polymer structures using particle swarm optimization technique. Theoretical Chemistry Accounts 143 (2024).
Published in , 1900
In the realm of studying supramolecular polymers using computer simulations, the task of generating appropriate initial structures poses a significant challenge, primarily owing to the extensive range of potential configurations. In this study, we introduce StackGen, an open-source framework designed to efficiently create energy-optimized one-dimensional supramolecular polymer structures with minimal computational overhead. This tool utilizes the particle swarm optimization (PSO) algorithm in conjunction with a semiempirical quantum mechanical approach to identify low-energy supramolecular stack configurations from a diverse set of possibilities. These configurations result from the translational and rotational adjustments of adjacent molecules around monomers along various axes. The tool also considers various structural factors, including the presence of functional side groups and the extent of intermolecular π-π stacking interactions. Extensive testing across different molecules demonstrates StackGen’s ability to produce low-energy structures with negligible computational costs. Additionally, the tool incorporates features for optimizing PSO hyperparameters in real-time, thus improving convergence. The tool provides a convenient means of generating structures suitable for both molecular simulations and quantum mechanical calculations.
S. R. Pramatha, D. Srideep, U. Pattnaik, R. Sahu, D. I. Suresh, A. C. Yadav, C. Muduli, S. K. Reddy, S. P. Senanayak, K. V. Rao, Secondary nucleation guided noncovalent synthesis of dendritic homochiral superstructures via growth on and from surface. Nature Communications 15 (2024).
Published in , 1900
Secondary nucleation is an emerging approach for synthesizing higher-order supramolecular polymers with exciting topologies. However, a detailed understanding of growth processes and the synthesis of homochiral superstructures is yet to be demonstrated. Here, we report the non-covalent synthesis of dendritic homochiral superstructures using NIR triimide dyes as building blocks via a secondary nucleation elongation process. Detailed analysis of kinetics and temporal evolution of morphology indicates that the formation of dendritic homochiral superstructures proceeds via growth on the surface and growth from the surface of the seeds. The combination of these two processes leads to the formation of elegant homochiral superstructures with a size of ~0.4 mm2, having a superhelix at the center and helical fibres as branches. Moreover, these dendritic homochiral superstructures exhibit significantly high chiro-optical photoresponse with the magnitude of gfactor reaching a value as high as 0.55 - 0.6. Thus, our results provide insights into the growth process of homochiral superstructures with dendritic topology, which can be critically important for the design and optimization of chiral-selective optoelectronic devices leveraging controlled self-assembly.
talks
Talk 1 on Relevant Topic in Your Field
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Conference Proceeding talk 3 on Relevant Topic in Your Field
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teaching
Teaching experience 1
Undergraduate course, University 1, Department, 2014
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Teaching experience 2
Workshop, University 1, Department, 2015
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