Repurposing DNA-binding agents as H-bonded organic semiconductors

Molecular analysis and design using generative artificial intelligence via multi-agent modeling

We report the use of a multiagent generative artificial intelligence framework, the X-LoRA-Gemma large language model (LLM), to analyze, design and test molecular design. The X-LoRA-Gemma model, inspired by biological principles and featuring 7 billion parameters, dynamically reconfigures its structure through a dual-pass inference strategy to enhance its problem-solving abilities across diverse scientific domains. The model is used to first identify molecular engineering targets through a systematic human-AI and AI-AI self-driving multi-agent approach to elucidate key targets for molecular optimization to improve interactions between molecules. Next, a multi-agent generative design process is used that includes rational steps, reasoning and autonomous knowledge extraction. Target properties of the molecule are identified either using a principal component analysis (PCA) of key molecular properties or sampling from the distribution of known molecular properties. The model is then used to generate a large set of candidate molecules, which are analyzed via their molecular structure, charge distribution, and other features. We validate that as predicted, increased dipole moment and polarizability is indeed achieved in the designed molecules. We anticipate an increasing integration of these techniques into the molecular engineering workflow, ultimately enabling the development of innovative solutions to address a wide range of societal challenges. We conclude with a critical discussion of challenges and opportunities of the use of multi-agent generative AI for molecular engineering, analysis and design.

Bioelectronics for bitterness-based phytocompound detection using human bitter taste receptor nanodiscs

Various organisms produce several products to defend themselves from the environment and enemies. These natural products have pharmacological and biological activities and are used for therapeutic purposes, retaining bitter taste because of chemical defense mechanisms. Cnicin is a plant-derived bitter sesquiterpene lactone with pharmacological characteristics such as anti-bacterial, anti-myeloma, anti-cancer, anti-tumor, anti-oxidant, anti-inflammatory, allelopathic, and cytotoxic properties. Although many studies have focused on cnicin detection, they have limitations and novel cnicin-detecting strategies are required. In this study, we developed the bioelectronics for screening cnicin using its distinct taste. hTAS2R46 was produced using an Escherichia coli expression system and reconstituted into nanodiscs (NDs). The binding sites and energy between hTAS2R46 and cnicin were investigated using biosimulations. hTAS2R46-NDs were combined with a side-gated graphene micropatterned field-effect transistor (SGMFET) to construct hTAS2R46-NDs bioelectronics. The construction was examined by chemical and electrical characterization. The developed system exhibited unprecedented performance, 10 fM limit of detection, rapid response time (within 10 s), 0.1354 pM-1 equilibrium constant, and high selectivity. Furthermore, the system was stable as the sensing performance was maintained for 15 days. Therefore, the hTAS2R46-NDs bioelectronics can be utilized to screen cnicin from natural products and applied in the food and drug industries.

Two-Step Synthesis of B2 N2 -Doped Polycyclic Aromatic Hydrocarbon Containing Pentagonal and Heptagonal Rings with Long-Lived Delayed Fluorescence

Pentagon-heptagon embedded polycyclic aromatic hydrocarbons (PAHs) have aroused increasing attention in recent years due to their unique physicochemical properties. Here, for the first time, this report demonstrates a facile method for the synthesis of a novel B2 N2 -doped PAH (BN-2) containing two pairs of pentagonal and heptagonal rings in only two steps. In the solid state of BN-2, two different conformations, including saddle-shaped and up-down geometries, are observed. Through a combined spectroscopic and calculation study, the excited-state dynamics of BN-2 is well-investigated in this current work. The resultant pentagon-heptagon embedded B2 N2 -doped BN-2 displays both prompt fluorescence and long-lived delayed fluorescence components at room temperature, with the triplet excited-state lifetime in the microsecond time region (τ = 19 µs). The triplet-triplet annihilation is assigned as the mechanism for the observed long-lived delayed fluorescence. Computational analyses attributed this observation to the small energy separation between the singlet and triplet excited states, facilitating the intersystem crossing (ISC) process which is further validated by the ultrafast spectroscopic measurements.

Technology Roadmap for Flexible Sensors

Humans rely increasingly on sensors to address grand challenges and to improve quality of life in the era of digitalization and big data. For ubiquitous sensing, flexible sensors are developed to overcome the limitations of conventional rigid counterparts. Despite rapid advancement in bench-side research over the last decade, the market adoption of flexible sensors remains limited. To ease and to expedite their deployment, here, we identify bottlenecks hindering the maturation of flexible sensors and propose promising solutions. We first analyze challenges in achieving satisfactory sensing performance for real-world applications and then summarize issues in compatible sensor-biology interfaces, followed by brief discussions on powering and connecting sensor networks. Issues en route to commercialization and for sustainable growth of the sector are also analyzed, highlighting environmental concerns and emphasizing nontechnical issues such as business, regulatory, and ethical considerations. Additionally, we look at future intelligent flexible sensors. In proposing a comprehensive roadmap, we hope to steer research efforts towards common goals and to guide coordinated development strategies from disparate communities. Through such collaborative efforts, scientific breakthroughs can be made sooner and capitalized for the betterment of humanity.

Multi-source transfer learning with Graph Neural Network for excellent modelling the bioactivities of ligands targeting orphan G protein-coupled receptors

G protein-coupled receptors (GPCRs) have been the targets for more than 40% of the currently approved drugs. Although neural networks can effectively improve the accuracy of prediction with the biological activity, the result is undesirable in the limited orphan GPCRs (oGPCRs) datasets. To this end, we proposed Multi-source Transfer Learning with Graph Neural Network, called MSTL-GNN, to bridge this gap. Firstly, there are three ideal sources of data for transfer learning, oGPCRs, experimentally validated GPCRs, and invalidated GPCRs similar to the former one. Secondly, the SIMLEs format GPCRs convert to graphics, and they can be the input of Graph Neural Network (GNN) and ensemble learning for improving prediction accuracy. Finally, our experiments show that MSTL-GNN remarkably improves the prediction of GPCRs ligand activity value compared with previous studies. On average, the two evaluation indexes we adopted, R2 and Root-mean-square deviation (RMSE). Compared with the state-of-the-art work MSTL-GNN increased up to 67.13% and 17.22%, respectively. The effectiveness of MSTL-GNN in the field of GPCR Drug discovery with limited data also paves the way for other similar application scenarios.

Ultrafast Dynamics and Photoresponse of a Fungi-Derived Pigment Xylindein from Solution to Thin Films

Organic semiconductor materials have recently gained momentum due to their non-toxicity, low cost, and sustainability. Xylindein is a remarkably photostable pigment secreted by fungi that grow on decaying wood, and its relatively strong electronic performance is enabled by π-π stacking and hydrogen-bonding network that promote charge transport. Herein, femtosecond transient absorption spectroscopy with a near-IR probe was used to unveil a rapid excited-state intramolecular proton transfer reaction. Conformational motions potentially lead to a conical intersection that quenches fluorescence in the monomeric state. In concentrated solutions, nascent aggregates exhibit a faster excited state lifetime due to excimer formation, confirmed by the excimer→charge-transfer excited-state absorption band of the xylindein thin film, thus limiting its optoelectronic performance. Therefore, extending the xylindein sidechains with branched alkyl groups may hinder the excimer formation and improve optoelectronic properties of naturally derived materials.

Structure-Property Relationships in Bithiophenes with Hydrogen-Bonded Substituents

The use of crystal engineering to control the supramolecular arrangement of π-conjugated molecules in the solid-state is of considerable interest for the development of novel organic electronic materials. In this study, we investigated the effect of combining of two types of supramolecular interaction with different geometric requirements, amide hydrogen bonding and π-interactions, on the π-overlap between calamitic π-conjugated cores. To this end, we prepared two series of bithiophene diesters and diamides with methylene, ethylene, or propylene spacers between the bithiophene core and the functional groups in their terminal substituents. The hydrogen-bonded bithiophene diamides showed significantly denser packing of the bithiophene cores than the diesters and other known α,ω-disubstituted bithiophenes. The bithiophene packing density reach a maximum in the bithiophene diamide with an ethylene spacer, which had the smallest longitudinal bithiophene displacement and infinite 1D arrays of electronically conjugated, parallel, and almost linear N-H⋅⋅⋅O=C hydrogen bonds. The synergistic hydrogen bonding and π-interactions were attributed to the favorable conformation mechanics of the ethylene spacer and resulted in H-type spectroscopic aggregates in solid-state absorption spectroscopy. These results demonstrate that the optoelectronic properties of π-conjugated materials in the solid-state may be tailored systematically by side-chain engineering, and hence that this approach has significant potential for the design of organic and polymer semiconductors.

Sensing a binding event through charge transport variations using an aromatic oligoamide capsule

The selective binding properties of a 13-mer oligoamide foldamer capsule composed of 4 different aromatic subunits are reported. The capsule was designed to recognize dicarboxylic acids through multiple-point interactions owing to a combination of protonation/deprotonation events, H-bonding, and geometrical constraints imparted by the rigidity of the foldamer backbone. Compared to tartaric acid, binding of 2,2-difluorosuccinic acid or 2,2,3,3-tetrafluorosuccinic acid resulted in symmetry breaking due to deprotonation of only one of the two carboxylic acid groups of the encapsulated species as shown by NMR studies in solution and by single-crystal X-ray diffraction in the solid state. An analogous 14-mer foldamer capsule terminated with a thiol anchoring group was used to probe the complexation event in self-assembled monolayers on Au substrates. Ellipsometry and polarization-modulation infrared absorption-reflection spectroscopy studies were consistent with the formation of a single molecule layer of the foldamer capsule oriented vertically with respect to the surface. The latter underwent smooth complexation of 2,2-difluorosuccinic acid with deprotonation of one of the two carboxylic acid groups. A significant (80-fold) difference in the charge transport properties of the monolayer upon encapsulation of the dicarboxylic acid was evidenced from conducting-AFM measurements (S = 1.1 × 10-9 vs. 1.4 × 10-11 ohm-1 for the empty and complexed capsule, respectively). The modulation in conductivity was assigned to protonation of the aromatic foldamer backbone.

Aggregation induced emission behavior in oleylamine acetone system and its application to get improved photocurrent from In2S3 quantum dots

Blue emission giving nanoscale molecular clusters of Oleylamine-Acetone system was formed by an aging assisted hydrogen bond formation between the interacting molecular systems, at room temperature. The as-formed nanoscale molecular clusters were found to be self-assembled into flower-like aggregates and shifted the emission wavelength to red colour depicting an exciton delocalization in the aggregate system. Interestingly aging process has also produced imine type binding between Oleylamine and Acetone due to the condensation reaction. The experimental conditions and formation mechanism of hydrogen bond assisted Oleylamine-Acetone molecular aggregates and imine bond assisted Oleylamine-Acetone is elaborated in this paper in a systematic experimental approach with suitable theory. Finally we have introduced this Acetone assisted aging process in In2S3 QD system prepared with Oleylamine as functional molecules. It was found that the aging process has detached Oleylamine from QD surface and as a consequence In2S3 QD embedded Oleylamine-Acetone aggregates was obtained. When this In2S3 QD embedded molecular cluster system was used as an active layer in a photo conductor device then a maximum photo current value of the order of milli Ampere was obtained. The surfactant molecules normally inhibit the charge transport between QD systems and as a result it is always problematic to have the functional molecules in the QD based transport devices. Our approach has a solution to this problem and the present paper discusses the outcome of the results in detail.

Hydrogen bond-rigidified planar squaraine dye and its electronic and organic semiconductor properties

The one-step reaction of a dicyanovinyl-functionalized squaric acid with Fischer bases afforded C2v symmetric squaraine dyes with rigid planar structures due to intramolecular N-HO hydrogen bonds. Dense molecular packing, decrease of HOMO level, and sufficient thermal stability for sublimation enabled vacuum-processed OTFTs with hole mobility up to 0.32 cm2 V-1 s-1 and current on/off ratio of 106.

Pushing property limits in materials discovery via boundless objective-free exploration

Our developed algorithm, BLOX (BoundLess Objective-free eXploration), successfully found “out-of-trend” molecules potentially useful for photofunctional materials from a drug database.

Materials chemists develop chemical compounds to meet often conflicting demands of industrial applications. This process may not be properly modeled by black-box optimization because the target property is not well defined in some cases. Herein, we propose a new algorithm for automated materials discovery called BoundLess Objective-free eXploration (BLOX) that uses a novel criterion based on kernel-based Stein discrepancy in the property space. Unlike other objective-free exploration methods, a boundary for the materials properties is not needed; hence, BLOX is suitable for open-ended scientific endeavors. We demonstrate the effectiveness of BLOX by finding light-absorbing molecules from a drug database. Our goal is to minimize the number of density functional theory calculations required to discover out-of-trend compounds in the intensity–wavelength property space. Using absorption spectroscopy, we experimentally verified that eight compounds identified as outstanding exhibit the expected optical properties. Our results show that BLOX is useful for chemical repurposing, and we expect this search method to have numerous applications in various scientific disciplines.

Repurposing of the anti-HIV drug emtricitabine as a hydrogen-bonded cleft for bipyridines via cocrystallization

Supramolecular repurposing of the anti-HIV drug emtricitabine enables the recognition of rod-shaped bipyridines as a hydrogen-bonded supramolecular cleft.