Molecular Modeling of Crystalline Alkylthiophene Oligomers and Polymers

Synthesis of novel (R)-carvone-tagged thiazolidinone as anticancer leads: characterization, in vitro antiproliferative evaluation and in silico studies

This work describes the successful synthesis of a series of three novel thiazolidinone-carvone-O-alkyl hybrids through a two-step approach involving heterocyclization and O-alkylation reactions. Comprehensive structural characterization of the obtained products was achieved using NMR and HRMS spectroscopic techniques. This study assessed in vitro antiproliferative activity of synthesized thiazolidinone-carvone-O-alkyl hybrids (5a-c) against various human cancer cell lines, viz. HT-1080 (fibrosarcoma), A-549 (lung cancer), MCF-7 (breast cancer) and MDA-MB-231 (breast cancer). MTT assay revealed promising results for compounds 5b and 5c, demonstrating good antiproliferative activity against A-549 and MCF-7 cell lines comparable to the positive control, Doxorubicin. Compound 5a, harbouring an O-acetoxy group, displayed limited anticancer activity against MCF-7 and MDA-MB-231 cells, with IC50 values of 69.33 ± 0.42 µM and >100 µM, respectively. Docking results confirmed that the compounds 5a-c binds at the active site of p21 with docking scores -2.0, -4.8, and -7.0 kcal/mol, respectively. Compound 5a-c also showed good binding potential against Bcl2 protein with docking score of -4.9, -6.0, -5.5 kcal/mol, respectively. Furthermore, binding energy analysis and dynamics simulation studies of compounds towards p21 and Bcl2 yielded promising results. In PAK4 assay, compound 5c showed comparable potency (IC50 6.76 µM) with the standard control UC2288 (IC50 6.40 µM), while in BCL-2 TR-FRET assay, 5c exhibited good inhibition (IC50 1.78 µM) as compared to Venetoclax (IC50 0.016 µM). In conclusion, compounds 5a-c could be used as a structural framework for the discovery of novel therapeutics to combat different types of cancer.Communicated by Ramaswamy H. Sarma.

Synthesis, crystal structure, spectroscopic characterization, DFT calculations, Hirshfeld surface analysis, molecular docking, and molecular dynamics simulation investigations of novel pyrazolopyranopyrimidine derivatives

A series of new pyrazolopyranopyrimidine derivatives (3-9) were synthesized from 5-amino-2,4-dihydro-3-methyl-4-phenylpyrano-[2,3-c]pyrazole-5-carbonitrile (2) by multicomponent reactions (MCR) involving malononitrile, benzaldehyde, and pyrazolone under refluxing ethanol in the presence of piperidine. Compound (2) was then converted to 2-acetylpyrazolopyranopyrimidine (3) through a reaction with acetic anhydride. The deprotection of 3 using ammonium hydroxide in ethanol, leads to 4. Subsequent chlorination of 4 by phosphorus oxychloride affords 5 which was alkylated using methyl iodide and ethyl bromoacetate in DMF, leading to regioisomers 6-9. The products were characterized by spectroscopic techniques (1H and 13C NMR) and confirmed by single crystal X-ray diffraction (XRD) studies for 2, 5, 6, and 9. Moreover, the geometrical parameters, molecular orbital calculations, and spectral data of 2, 5, 6, and 9 were compared by DFT at the B3LYP/6-311G(d,p) level of theory. There is good agreement between the calculated results and the experimental data. The intermolecular contacts for 2, 5, 6, and 9 were studied by Hirshfeld surface analysis. In addition, the molecular docky study was conducted to investigate the binding patterns of 2, 5, 6, and 9 within the binding site of cyclin-dependent kinase 2 (CDK2) and penicillin-binding protein 1 A. After the docking process, molecular dynamics (MD) simulations for 100 ns were performed on CDK2 and PBP 1 A proteins in the complex with 5.Communicated by Ramaswamy H. Sarma.

Enhanced Photovoltaic Properties of Y6 Derivatives with Asymmetric Terminal Groups: A Theoretical Insight

Y6 derivatives with asymmetric terminal groups have attracted considerable attention in recent years. However, the effects of the asymmetric modification of terminal groups on the photovoltaic performance of Y6 derivatives are not well understood yet. Therefore, we designed a series of Y6-based acceptors with asymmetric terminal groups by endowing them with various electron-withdrawing abilities and different conjugated rings to conduct systematic research. The electron-withdrawing ability of the Y6-D1 terminal group (substituted by IC-2F and IC-2NO2 terminals) is strongest, followed by Y6 (substituted by two same IC-2F terminals), Y6-D2 (substituted by IC-2F and 2-(4-oxo-4,5-dihydro-6H-cyclopenta[b]thiophen-6-ylidene)malononitrile terminals), Y6-D4 (substituted by IC-2F and indene ring), and Y6-D3 (substituted by IC-2F and thiazole ring). Computed results show that A-A stacking is the main molecular packing mode of Y6 and four other asymmetric Y6 derivatives. The ratios of A-A stacking face-on configuration of Y6-D1, Y6-D2, Y6-D3, Y6-D4, and Y6 are 51.6%, 55.0%, 43.5%, 59.3%, and 62.4%, respectively. Except for Y6-D1 substituted by the IC-2F and IC-2NO2 (the strongest electron-withdrawing capacity) terminal groups, the other three asymmetric molecules are mainly electron-transporting and can therefore act as acceptors. The open-circuit voltages of organic solar cells (OSCs) based on Y6-D2, Y6-D3, and Y6-D4, except for Y6-D1, may be higher than those of OSCs based on the Y6 acceptor because of their higher energy levels of lowest unoccupied molecular orbital (LUMO). PM6/Y6-D3 and PM6/Y6-D4 have better light absorption properties than PM6/Y6 due to their higher total oscillator strength. These results indicate that Y6-D3 and Y6-D4 can be employed as good acceptors.

The Effect of Glycol Side Chains on the Assembly and Microstructure of Conjugated Polymers

Conjugated polymers with glycol-based chains, are emerging as a material class with promising applications as organic mixed ionic-electronic conductors, particularly in bioelectronics and thermoelectrics. However, little is still known about their microstructure and the role of the side chains in determining intermolecular interactions and polymer packing. Here, we use the combination of electrospray deposition and scanning tunneling microscopy to determine the microstructure of prototypical glycolated conjugated polymers (pgBTTT and p(g2T-TT)) with submonomer resolution. Molecular dynamics simulations of the same surface-adsorbed polymers exhibit an excellent agreement with the experimental images, allowing us to extend the characterization of the polymers to the atomic scale. Our results prove that, similarly to their alkylated counterparts, glycolated polymers assemble through interdigitation of their side chains, although significant differences are found in their conformation and interaction patterns. A model is proposed that identifies the driving force for the polymer assembly in the tendency of the side chains to adopt the conformation of their free analogues, i.e., polyethylene and polyethylene glycol, for alkyl or ethylene glycol side chains, respectively. For both classes of polymers, it is also demonstrated that the backbone conformation is determined to a higher degree by the interaction between the side chains rather than by the backbone torsional potential energy. The generalization of these findings from two-dimensional (2D) monolayers to three-dimensional thin films is discussed, together with the opportunity to use this type of 2D study to gain so far inaccessible, subnm-scale information on the microstructure of conjugated polymers.

Impact of Side-Chain Hydrophilicity on Packing, Swelling, and Ion Interactions in Oxy-Bithiophene Semiconductors

Exchanging hydrophobic alkyl-based side chains to hydrophilic glycol-based side chains is a widely adopted method for improving mixed-transport device performance, despite the impact on solid-state packing and polymer-electrolyte interactions being poorly understood. Presented here is a molecular dynamics (MD) force field for modeling alkoxylated and glycolated polythiophenes. The force field is validated against known packing motifs for their monomer crystals. MD simulations, coupled with X-ray diffraction (XRD), show that alkoxylated polythiophenes will pack with a "tilted stack" and straight interdigitating side chains, whilst their glycolated counterpart will pack with a "deflected stack" and an s-bend side-chain configuration. MD simulations reveal water penetration pathways into the alkoxylated and glycolated crystals-through the π-stack and through the lamellar stack respectively. Finally, the two distinct ways triethylene glycol polymers can bind to cations are revealed, showing the formation of a metastable single bound state, or an energetically deep double bound state, both with a strong side-chain length dependence. The minimum energy pathways for the formation of the chelates are identified, showing the physical process through which cations can bind to one or two side chains of a glycolated polythiophene, with consequences for ion transport in bithiophene semiconductors.

Influence of Asphaltene Modification on Structure of P3HT/Asphaltene Blends: Molecular Dynamics Simulations

Further development and commercialization of bulk heterojunction (BHJ) solar cells require the search for novel low-cost materials. The present study addresses the relations between the asphaltenes' chemical structure and the morphology of the poly(3-hexylthiohene) (P3HT)/asphaltene blends as potential materials for the design of BHJ solar cells. By means of all-atom molecular dynamics simulations, the formation of heterophase morphology is observed for the P3HT-based blends with carboxyl-containing asphaltenes, as well as the aggregation of the asphaltenes into highly ordered stacks. Although the π-π interactions between the polyaromatic cores of the asphaltenes in solutions are sufficient for the molecules to aggregate into ordered stacks, in a blend with a conjugated polymer, additional stabilizing factors are required, such as hydrogen bonding between carboxyl groups. It is found that the asphaltenes' aliphatic side groups may improve significantly the miscibility between the polymer and the asphaltenes, thereby preventing the formation of heterophase morphology. The results also demonstrate that the carboxyl-containing asphaltenes/P3HT ratio should be at least 1:1, as a decrease in concentration of the asphaltenes leads to the folding of the polymer chains, lower ordering in the polymer phase and the destruction of the interpenetrating 3D structure formed by P3HT and the asphaltene phases. Overall, the results of the present study for the first time reveal the aggregation behavior of the asphaltenes of varying chemical structures in P3HT, as well the influence of their presence and concentration on the polymer phase structure and blend morphology, paving the way for future development of BHJ solar cells based on the conjugated polymer/asphaltene blends.

Development of hybrid coarse-grained atomistic models for rapid assessment of local structuring of polymeric semiconductors

Decades of work in the field of computational study of semiconducting polymers using atomistic models illustrate the challenges of generating equilibrated models for this class of materials. While adopting a coarse-grained model can be helpful, the process of developing a suitable model is particularly non-trivial and time-consuming for semiconducting polymers due to a large number of different interactions with some having an anisotropic nature. This work introduces a procedure for the rapid generation of a hybrid model for semiconducting polymers where atoms of secondary importance (those in the alkyl side chains) are transformed into coarse-grained beads to reduce the computational cost of generating an equilibrated structure. The parameters are determined from easy-to-equilibrate simulations of very short oligomers and the model is constructed to enable a very simple back-mapping procedure to reconstruct geometries with atomistic resolution. The model is illustrated for three related polymers containing DPP (diketopyrrolopyrrole) to evaluate the transferability of the potential across different families of polymers. The accuracy of the model, determined by comparison with the results of fully equilibrated simulations of the same material before and after back-mapping, is fully satisfactory for two out of the three cases considered. We noticed that accuracy can be determined very early in the workflow so that it is easy to assess when the deployment of this method is advantageous. The hybrid representation can be used to evaluate directly the electronic properties of structures sampled by the simulations.

Strategies for the Development of Conjugated Polymer Molecular Dynamics Force Fields Validated with Neutron and X-ray Scattering

Conjugated polymers (CPs) enable a wide range of lightweight, lower cost, and flexible organic electronic devices, but a thorough understanding of relationships between molecular structure and dynamics and electronic performance is critical for improved device efficiencies and for new technologies. Molecular dynamics (MD) simulations offer in silico insight into this relationship, but their accuracy relies on the approach used to develop the model's parameters or force field (FF). In this Perspective, we first review current FFs for CPs and find that most of the models implement an arduous reparameterization of inter-ring torsion potentials and partial charges of classical FFs. However, there are few FFs outside of simple CP molecules, e.g., polythiophenes, that have been developed over the last two decades. There is also limited reparameterization of other parameters, such as nonbonded Lennard-Jones interactions, which we find to be directly influenced by conjugation in these materials. We further provide a discussion on experimental validation of MD FFs, with emphasis on neutron and X-ray scattering. We define multiple ways in which various scattering methods can be directly compared to results of MD simulations, providing a powerful experimental validation metric of local structure and dynamics at relevant length and time scales to charge transport mechanisms in CPs. Finally, we offer a perspective on the use of neutron scattering with machine learning to enable high-throughput parametrization of accurate and experimentally validated CP FFs enabled not only by the ongoing advancements in computational chemistry, data science, and high-performance computing but also using oligomers as proxies for longer polymer chains during FF development.

Properties of Conjugated Materials from Quantum Chemistry Coupled to Molecular Dynamics Generated Ensembles

We provide a set of molecular dynamics simulations employing a force field specifically parameterized for organic π-conjugated materials. The resulting conformation ensemble was coupled to quantum chemistry calculations, and quantities of interest for optoelectronic applications, namely, ground- and excited-state energies, oscillator strengths, and dipole moments were extracted. This combined approach allowed not only exploration of the configurational landscape but also of the resulting electronic properties of each frame within the simulation and thus probe the link between conformation and property. A study was made of the sampling and convergence requirements to yield reliable averages over the ensemble. Typically between 800 and 1000 conformations were sufficient to ensure convergence of properties. However, for some oligomers, more configurations were required to achieve convergence of the oscillator strength and magnitude of the dipole moment.

From flat to tilted: gradual interfaces in organic thin film growth

We investigate domain formation and local morphology of thin films of α-sexithiophene (α-6T) on Au(100) beyond monolayer coverage by combining high resolution scanning tunneling microscopy (STM) experiments with electronic structure theory calculations and computational structure search. We report a layerwise growth of highly-ordered enantiopure domains. For the second and third layer, we show that the molecular orbitals of individual α-6T molecules can be well resolved by STM, providing access to detailed information on the molecular orientation. We find that already in the second layer the molecules abandon the flat adsorption structure of the monolayer and adopt a tilted conformation. Although the observed tilted arrangement resembles the orientation of α-6T in the bulk, the observed morphology does not yet correspond to a well-defined surface of the α-6T bulk structure. A similar behavior is found for the third layer indicating a growth mechanism where the bulk structure is gradually adopted over several layers.

Assessment of molecular dynamics simulations for amorphous poly(3-hexylthiophene) using neutron and X-ray scattering experiments

The molecular morphology and dynamics of conjugated polymers in the bulk solid state play a significant role in determining macroscopic charge transport properties. To understand this relationship, molecular dynamics (MD) simulations and quantum mechanical calculations are used to evaluate local electronic properties. In this work, we investigate the importance of system and simulation parameters, such as force fields and equilibration methods, when simulating amorphous poly(3-hexylthiophene) (P3HT), a model semiconducting polymer. An assessment of MD simulations for five different published P3HT force fields is made by comparing results to experimental wide-angle X-ray scattering (WAXS) and to a broad range of quasi-elastic neutron scattering (QENS) data. Moreover, an in silico analysis of force field parameters reveals that atomic partial charges and torsion potentials along the backbone and side chains have the greatest impact on structure and dynamics related to charge transport mechanisms in P3HT.

Atomistic modelling of entropy driven phase transitions between different crystal modifications in polymers: the case of poly(3-alkylthiophenes)

Polymorphism and related solid-state phase transitions affect the structure and morphology and hence the properties of materials, but they are not-so-well understood. Atomistic computational methods can provide molecular-level insights, but they have rarely proven successful for transitions between polymorphic forms of crystalline polymers. In this work, we report atomistic molecular dynamics (MD) simulations of poly(3-alkylthiophenes) (P3ATs), widely used organic semiconductors to explore the experimentally observed, entropy-driven transition from form II to more common form I type polymorphs, or, more precisely, to form I mesophases. The transition is followed continuously, also considering X-ray diffraction evidence, for poly(3-hexylthiophene) (P3HT) and poly(3-butylthiophene) (P3BT), evidencing three main steps: (i) loss of side chain interdigitation, (ii) partial disruption of the original stacking order and (iii) reorganization of polymer chains into new, tighter, main-chain stacks and new layers with characteristic form I periodicities, substantially larger than those in the original form II. The described approach, likely applicable to other important transitions in polymers, provides previously inaccessible insight into the structural organization and disorder features of form I structures of P3ATs, not only in their development from form II structures but also from melts or solutions.

The correspondence between the conformational and chromophoric properties of amorphous conjugated polymers in mesoscale condensed systems

For π-conjugated polymers, the notion of spectroscopic units or "chromophores" provides illuminating insights into the experimentally observed absorption/emission spectra and the mechanisms of energy/charge transfer. To date, however, no statistical analysis has revealed a direct correspondence between chromophoric and conformational properties-with the latter being fundamental to polymer semiconductors. Herein, we propose a "persistence length" calculation to re-evaluate chain conformation over a full conjugation length. The mesoscale condensed systems of MEH-PPV and MEH-PPV/C₆₀ hybrid (system size ∼10 × 10 × 10 nm³) are utilized as two prototypical model systems, along with a full range of segmental lengths (2-20-mer) and five lowest singlet excited states to hint at the generality of the features presented. We demonstrate, for the first time, that two properly re-defined conformational factors that characterize chain folding and planarity, respectively, capture excellently the population distribution of chromophores in both systems investigated. In contrast, the conventional strategy of utilizing two adjacent monomer units to characterize (local) chain conformation results in only an inconspicuous correlation between the two, as previously reported. It is further shown that chain folding-and not chain planarity-is more relevant in capturing the associated oscillator strength for the first excited state, where the transient dipole moments are known to align with the chain conformation, although the corresponding excitation energy and exciton size seem relatively unaffected. The observed effects of C₆₀ on the MEH-PPV adsorption spectra also agree with recent experimental trends. Overall, the present findings are expected to aid future multiscale computer simulations and spectroscopy-data interpretations for polymer semiconductors and their hybrid systems.

Effects of bromination of poly(3-hexylthiophene) on the performance of bulk heterojunction solar cells

Through partial bromination of P3HT, we examined the effects of π-electron delocalization on the solar cell performance. A higher Br concentration restricts first intra- and then inter-chain delocalization, disrupting charge transport channels.

Systems biology-based discovery of a potential Atg4B agonist (Flubendazole) that induces autophagy in breast cancer

The aim of this study was to explore the autophagy-related protein 4B(ATG4B) and its targeted candidate agonist in triple-negative breast cancer (TNBC) therapy. In this study, the identification of Atg4B as a novel breast cancer target for screening candidate small molecular agonists was performed by phylogenetic analysis, network construction, molecular modelling, molecular docking and molecular dynamics (MD) simulation. In vitro, MTT assay, electron microscopy, western blot and ROS measurement were used for validating the efficacy of the candidate compounds. We used the phylogenetic analysis of Atg4B and constructed their protein-protein interaction (PPI) network. Also, we screened target compounds of Atg4 proteins from Drugbank and ZINC. Flubendazole was validated for its anti-proliferative efficacy in MDA-MB-231 cells. Further MD simulation results supported the stable interaction between Flubendazole and Atg4B. Moreover, Flubendazole induced autophagy and increased ROS production. In conclusion, in silico analysis and experimental validation together demonstrate that Flubendazole can target Atg4B in MDA-MB-231 cells and induce autophagy, which may shed light on the exploration of this compound as a potential new Atg4B targeted drug for future TNBC therapy.

Optical properties of regioregular poly(3-hexylthiophene) aggregates from fully atomistic investigations

We report on a first-principle theoretical investigation of the optical absorption and emission spectra of poly(3-hexylthiophene) (P3HT) aggregates by means of a multiscale all-atom hybrid approach, which combines molecular dynamics simulations, quantum-chemical calculations, and solving of a Frenkel–Holstein model.

Structure of P3HT crystals, thin films, and solutions by UV/Vis spectral analysis

The shift in the absorption spectrum of P3HT when comparing solution, spin-coated thin films, and the bulk crystal can be reproduced by multiscale simulation and explained in terms of the degree of intramolecular torsion.

Effects of thermal disorder on the electronic properties of ordered polymers

Main chain disorder is mainly responsible for localisation of HOMO states, while side chain disorder also has a pronounced effect.

Parameter free calculation of the subgap density of states in poly(3-hexylthiophene)

We investigate the influence of intra-chain and inter-chain interactions on the sub-gap density of states in a conjugated polymer using a combination of atomistic molecular dynamics simulation of polymer film structure and tight-binding calculation of electronic energy levels. For disordered assemblies of poly-3-hexylthiophene we find that the tail of the density of hole states is approximately exponential with a characteristic energy of 37 meV, which is similar to experimental values. This tail of states arises mainly from variations in the electronic coupling between neighbouring monomers, and is only slightly influenced by interchain coupling. Thus, knowledge of the disorder in torsion between neighbouring monomers is sufficient to estimate the density of states for the polymer. However, the intrachain torsional disorder is determined largely by the packing of the chains rather than the torsional potential alone. We propose the combination of methods as a tool to design higher mobility conjugated polymers.

Improved force field for molecular modeling of poly(3-hexylthiophene)

An ab initio-based improved force field is reported for poly(3-hexylthiophene) (P3HT) in the solid state, deriving torsional parameters and partial atomic charges from ab initio molecular structure calculations with explicit treatment of the hexyl side chains. The force field is validated by molecular dynamics (MD) simulations of solid P3HT with different molecular weights including calculation of structural parameters, mass density, melting temperature, glass transition temperature, and surface tension. At 300 K, the P3HT crystalline structure features planar backbones with non-interdigitated all-trans hexyl side chains twisted ~90° from the plane of the backbone. For crystalline P3HT with infinitely long chains, the calculated 300 K mass density (1.05 g cm(-3)), the melting temperature (490 K), and the 300 K surface tension (32 mN/m) are all in agreement with reported experimental values, as is the glass transition temperature (300 K) for amorphous 20-mers.

Theoretical study of torsional disorder in poly(3-alkylthiophene) single chains: intramolecular charge-transfer character and implications for photovoltaic properties

The role of polymer chain morphology on the optoelectronic properties of polythiophenes is an ongoing investigation with the promise of improving organic photovoltaic performance. Chain morphology is predominantly affected by torsional disorder, which causes localization of holes and electrons in the conjugated backbone. Using the model compound oligo(3-methylthiophene), torsionally disordered oligomers were created to compare with a trans-planar oligomer such as found in crystalline poly(3-hexylthiophene). Low lying electronic excitations are calculated using TD-HF and TD-DFT with various long-range corrected functionals. Probability densities of electron and hole were constructed from natural transition orbitals, giving insight into localization and electron-hole overlap. Overlap is found to be substantially higher in disordered oligomers, indicating a stronger Coulombic interaction between electron and hole. Results suggest that improved photovoltaic performance with increased crystallinity is partially explained by stronger light absorption in crystalline polymers and a higher barrier to charge separation in disordered polymers.

Probing the relation between charge transport and supramolecular organization down to ångström resolution in a benzothiadiazole-cyclopentadithiophene copolymer

Molecular modeling shows that longitudinal displacement of the backbones by a couple of ångströms has a profound impact on the electronic coupling mediating charge transport in a conjugated copolymer. These changes can be probed by monitoring the calculated X-ray scattering patterns and NMR chemical shifts as a function of sliding of the polymer chains and comparing them to experiment.