The Memory Palace

Reading List

Like a todo-list but for knowledge. Ideally this page is auto-updated by the curating agent every morning as it reads the arXiv feeds…

12 Feb 2025

  • Single molecule peptide synthesis without any side-chain protection using a nanopore and a sub-nanometer positioning system
    G, Sampath
    Organic Chemistry on ChemRxiv
    2025-02-11
     The paper presents a method for single-molecule peptide synthesis without side-chain protection using a nanopore with a sub-nanometer positioning system. The method allows for N-to-C or C-to-N synthesis, minimizes reagent usage, and reduces post-synthesis cleanup. It offers potential for large-scale synthesis with an array of headers and nanopores, achieving high precision and greenness.

  • Pseudo-4-Component Photoredox-catalyzed Alkylative Amidination / Carbamoylation of Styrenes with Isocyanides and Redox-Active Esters
    Maxime R., Vitale; Alexandre, Simon; Camilla, Acconcia; Sylvestre P. J. T., Bachollet; Mariateresa, Giustiniano; Laurence, Grimaud; Jérémy, Forté; Virgile, Rouffeteau
    Organic Chemistry on ChemRxiv
    2025-02-11
     The paper presents a photoredox-catalyzed process for alkylative amidination of styrenes, utilizing isocyanides and redox-active esters (RAEs). This method demonstrates broad functional group tolerance, allowing the final products, amidines, to be converted into various derivatives. The study showcases a novel synthetic approach with versatile applications in organic chemistry.

  • Au(III)-Catalyzed Domino Cyclization / Functionalization Reactions: an Efficient Entry to Heterocycles
    Antoine, Versini; Quentin, Arias; Jonathan, Boyer; Sandra, Olivero; Etienne, Brachet; Philippe, Belmont; Véronique, Michelet
    Organic Chemistry on ChemRxiv
    2025-02-11
     The paper discusses a gold(III)-catalyzed method for domino cyclization and functionalization, facilitating the synthesis of highly functionalized polyheterocycles. It focuses on creating isochromenes from 2-ethynylarylaldehydes and cycloisomerizing 1,6-enynes. The use of NHC-type gold(III) catalysts demonstrated superior reactivity and tolerance to functional groups compared to gold(I) catalysts.

  • Beyond HAT: Harnessing TBADT for photocatalyzed C(sp3)-C(sp3) Bond Formation through Reductive SET
    MAURIZIO, FAGNONI; Matteo, Leone; Dalila, Arnaldi
    Organic Chemistry on ChemRxiv
    2025-02-11
     This paper explores the use of the decatungstate anion (TBADT) for photocatalyzed C(sp3)-C(sp3) bond formation via reductive single electron transfer (SET). By optimizing conditions with γ-terpinene as a hydrogen donor, the method achieves high yields in alkylations of olefins, demonstrating TBADT’s potential in sustainable organic synthesis and pharmaceutical applications.

  • Genie in a Bottle – Formation and Reactivity of an Elusive Monomeric Mn(IV)-Oxo Species Inside a Cavitand Pore
    Yuri, Tulchinsky; Galon, Green; Kamal Uddin, Ansari; Daphna, Shimon; Thejasree, Munikrishna; Sagi, Ezov; Donia, Shamali; Orit, Cohen
    Organic Chemistry on ChemRxiv
    2025-02-11
     The paper discusses a novel cavitand architecture with a Mn(II) center that generates a highly reactive Mn(IV)-oxo species. This species was characterized using spectroscopy and XRD, supported by ab-initio/TDDFT calculations. The study reveals the reactivity of the Mn(IV)-oxo core in H atom abstraction and O atom transfer, showcasing regioselective oxidation similar to natural metalloenzymes.

  • Asymmetric Electrochemical Alkenylation by Synergistic Chiral Primary Amine and Naphthalene Catalysis
    Yingdong, Duan; Jianyuan, Chen; Liang, Cheng; Sanzhong, Luo
    Organic Chemistry on ChemRxiv
    2025-02-11
     The paper presents a method for asymmetric α-alkenylation of carbonyl compounds using potassium alkenyl trifluoroborate under electrochemical conditions, enhancing reactivity with the new organic mediator dimethoxyl naphthalene. Mechanistic studies reveal an ion-pair interaction contributing to high enantioselectivity, achieving unprecedented levels of enantioselectivities in electro-oxidative enamine transformations.

11 Feb 2025

  • Machine Learning-Driven Discovery of Highly Selective Antifungal Peptides Containing Non-Canonical β-Amino Acids
    Reid, Van Lehn; Sean, Palecek; David, Lynn; Myung-Ryul, Lee; Douglas, Chang; Joshua, Richardson
    Biological and Medicinal Chemistry on ChemRxiv
    2025-02-10
     The paper presents an iterative Gaussian process regression (GPR) method for the discovery of antifungal peptides with improved selectivity. Using a dataset of 147 sequences and their activities, the researchers explored 336,000 synthetic analogues of aurein 1.2, achieving up to 52-fold increased selectivity. This approach integrates computational predictions with experimental validation to combat antimicrobial resistance.

  • Probability Guided Chemical Reaction Scopes
    Inbal Lorena, Eshel; Barkai, Shahar; Sergio , Barranco; Mónica, Pérez-Temprano; Anat, Milo
    Organic Chemistry on ChemRxiv
    2025-02-10
     The paper presents a method for classifying chemical substrates based on reaction conditions to enhance synthetic protocol design. It uses a probability estimation approach that compares molecular features of target substrates with reported ones. This method is suitable for small datasets, addressing the challenge of low substrate diversity in existing literature.

  • Programmable Strategies for the Conversion of Aldehydes to Unsymmetrical (Deuterated) Diarylmethanes and Diarylketones
    Ahmad, Masarwa; Vipin, Gavit; Nicole, Hanania; Nadim, Eghbarieh; Israa, Shioukhi
    Organic Chemistry on ChemRxiv
    2025-02-10
     The study presents an efficient method for synthesizing unsymmetrical diarylmethanes and diarylketones using aldehydes and arenes. Key techniques include regioselective Ar-H alkylation and chemoselective reductions or oxidations of phosphonium salts. The synthesis of fully deuterated diarylmethanes using D2O is highlighted. High yields and simple setups indicate its potential for academic and pharmaceutical applications.

  • Synthesis of an ultra-bright rotaxane with threaded BODIPY stoppers
    Yann, Trolez; Matthieu, Hicguet; Olivier, Mongin; Fabienne, Berrée
    Organic Chemistry on ChemRxiv
    2025-02-10
     The paper reports the synthesis of two boron-assembled rotaxanes, featuring threaded BODIPY stoppers. One rotaxane achieved highly efficient fluorescence (quantum yield of 64%) upon selective boron removal, resulting in a brightness of 1.24 x 10^5 mol^-1.L.cm^-1, making it among the brightest reported. The method involved using potassium hydroxide for selective boron removal.

  • Selective Phosphorylation of Phenols and Benzenediols by the Kinase PsiK and Variants Thereof
    Jared, Lewis; Ahram, Kim; Nicolás M., Morato; R. Graham, Cooks; Ryan M., Phelan; Prabir, Saha; Pascal, Eyimegwu; Aqeel A., Niyaz; Rui, Huang
    Organic Chemistry on ChemRxiv
    2025-02-10
     The paper investigates the kinase PsiK’s ability to selectively phosphorylate phenols and benzenediols. Utilizing ATP as a phosphate donor, the study shows PsiK effectively phosphorylates various substituted phenols and benzenediols, achieving gram-scale phosphorylation with a turnover number exceeding 10,000. The findings suggest potential synthetic applications for this biocatalytic method.

  • Unusual Directionality in Thioamide Hydrogen Bonds Can Stabilize β-Strands
    Haoliang, Zheng; Robert W, Newberry
    Organic Chemistry on ChemRxiv
    2025-02-10
     The paper investigates how thioamides, despite being weaker hydrogen-bond acceptors, can stabilize β-strands through unusual directionality in hydrogen bonding. Using spectroscopic analysis of minimal amino-acid models and β-hairpin models, the study confirms these effects and suggests potential control over β-strand stability through thioamide incorporation.

  • Aryl Thiocyanate as an Organic ‘CN’ Source: Circular Chemical Economy Approach to Access Thiocyano-Thioesters from Cyclic Thioacetals
    Dr. Ramakrishna G., Bhat; Mousumi, Behera; Shubham , Shukla; Pankaj D. , Dharpure
    Organic Chemistry on ChemRxiv
    2025-02-10
     The paper discusses a mild, transition metal-free method using aryl thiocyanate to produce thiocyano-thioesters from cyclic thioacetals via organophotoredox catalysis. It emphasizes a circular chemical economy by repurposing diaryl disulfide as a reusable substrate. The method shows broad functional group tolerance and scalability, supported by control experiments and cyclic voltammetry analysis.

  • Direct activation of C(sp3)–H bonds by carbon dots photoredox catalysts
    Le, Wang; Yuyong, Ma; Meifang, Zhu; Mingwei, Hui; Di, Chen; Dingxi, Li; Xianhao, Chi; Keping, Zhai
    Organic Chemistry on ChemRxiv
    2025-02-10
     The paper presents the innovative use of carbon dots (CDs) as metal-free photoredox catalysts for functionalizing C(sp³)–H bonds. It highlights their tunable photophysical properties that enhance reactivity, enabling a switch between Giese radical addition and dehydrogenative annulation. The findings demonstrate the potential of CDs for sustainable organic synthesis, addressing the limitations of precious metal catalysts.

08 Feb 2025

  • Recent Advances in Machine Learning and Coarse-Grained Potentials for Biomolecular Simulations and Their Applications
    Leonardo, Medrano Sandonas, Adolfo, B. Poma, Alejandra, Hinostroza Caldas, Luis, Cofas-Vargas, Michael, Jones, Andrew, L. Ferguson
    Biological and Medicinal Chemistry on ChemRxiv
    2025-02-07
     The paper reviews advancements in machine learning (ML) and coarse-grained (CG) potentials for biomolecular simulations, addressing the challenges of multiscale biological processes. It highlights ML-driven potentials with quantum accuracy and backmapping techniques, enhancing simulation efficiency while maintaining accuracy. These developments aim to improve insights in drug discovery and virus-host interactions by extending time and length scales in simulations.

  • Assigning the Stereochemistry of Natural Products by Machine Learning
    Jean-Louis, Reymond, Markus, Orsi
    Biological and Medicinal Chemistry on ChemRxiv
    2025-02-07
     The paper presents NPstereo, a machine learning model trained on the COCONUT database, which assigns the stereochemistry of natural products (NPs) with 80.1% accuracy for full assignments and 86.3% for partial assignments. It effectively translates NP structures into isomeric SMILES notation, aiding in the characterization of secondary metabolites like alkaloids and polyketides.

  • Text2Struc: Programmatic Crystal Structure Generation with Fine-Tuned Large Language Models
    Viktoriia, Baibakova, Weike, Ye, Igor, Vasiljevic, Steven, Torrisi
    Theoretical and Computational Chemistry on ChemRxiv
    2025-02-07
     The paper presents Text2Struc, a fine-tuned CodeGen model for generating crystal structures from text. It utilizes low-rank adaptation and compares outputs to the Materials Project database. Results indicate that API calls yield higher accuracy, especially for complex structures, while training without CIF outputs increases generation fidelity. The findings emphasize the benefits of fine-tuning and API integration in materials science automation.

  • Chemical functionalization of a unique 2D material – Computational prediction for cyclooctyne on the biphenylene network
    Ralf, Tonner-Zech, Hendrik, Weiske
    Theoretical and Computational Chemistry on ChemRxiv
    2025-02-07
     This paper employs density functional theory to predict the chemical functionalization of the biphenylene network with cyclooctyne. The study reveals an asynchronous [2+2] cycloaddition mechanism that alters the effective band structure, leading to unique electronic properties. The research highlights the high reactivity of the biphenylene network, signifying its potential for novel functional materials.

  • Hierarchical Transfer Learning: An Agile and Equitable Strategy for Machine-Learning Interatomic Models
    Rebecca, Lindsey, Awwal, Oladipupo, Sorin, Bastea, Bradley, Steele, I-Feng William, Kuo, Nir, Goldman
    Theoretical and Computational Chemistry on ChemRxiv
    2025-02-07
     The paper presents a hierarchical transfer learning approach for machine-learned interatomic models (ML-IAM) to efficiently handle complex systems with multiple element types. Demonstrated on C and N mixtures at various conditions, it allows for reusable parameter blocks, enhancing model generation accessibility and validation while reducing computational demands on users.

07 Feb 2025

  • Single-Molecule Quantification of RNA Degradation with Nanopore Sensing
    Casey, Platnich; Mohammed, Alawami; Max, Earle; Ulrich, Keyser
    Biological and Medicinal Chemistry on ChemRxiv
    2025-02-07
     The paper introduces solid-state nanopore sensing as a novel method for quantifying RNA degradation, offering single-molecule resolution for very low RNA quantities (as little as 100 pg). This method outperforms gel electrophoresis, which requires larger amounts of RNA. The results indicate nanopore sensing is effective for analyzing RNA integrity in challenging samples.

  • Going nuclear: Improved antisense oligonucleotide activity through conjugation with a nuclear importer
    Michael, Booth; Thomas, Milne; Disha, Kashyap
    Biological and Medicinal Chemistry on ChemRxiv
    2025-02-06
     The paper discusses the enhancement of antisense oligonucleotide (ASO) efficacy through conjugation with the nuclear importer (+)-JQ1. This method improved the performance of ASOs, particularly Oblimersen, in nuclear delivery, splice-switching, and mRNA knockdown. The findings suggest that modifying ASOs with nuclear importers may lead to more effective therapeutics.

  • AlphaFold2-RAVE: Protein Ensemble Generation with Physics-Based Sampling
    Da, Teng; Vanessa J., Meraz; Akashnathan, Aranganathan; Xinyu, Gu; Pratyush, Tiwary
    Biological and Medicinal Chemistry on ChemRxiv
    2025-02-06
     The paper presents AlphaFold2-RAVE, an open-source Python package that combines AlphaFold2 predictions with molecular dynamics simulations for efficient protein ensemble generation. It utilizes a feature selection module and the State Predictive Information Bottleneck method for structural analysis. Validation on proteins like E. coli adenosine kinase and the SARS-CoV-2 spike protein shows high sampling efficiency and minimal computational cost, promoting applications in drug discovery.

  • Discovery of amodiachins, a novel class of 4-aminoquinoline antimalarials active against multi-drug resistant Plasmodium falciparum
    Mason J, Handford; Yuexin, Li; Terry, Riscoe; Katherine, Liebman; Michael K, Riscoe
    Biological and Medicinal Chemistry on ChemRxiv
    2025-02-06
     The paper explores amodiachin analogs as new 4-aminoquinoline antimalarials against multi-drug resistant Plasmodium falciparum. A series of synthesized compounds were tested for activity in cultured erythrocytes and cytotoxicity in HepG2 cells. Notably, compound 43 (ADC-028) showed potent antimalarial effects with significant metabolic stability and low toxicity, suggesting its potential in treating malaria.

  • Co-Design of Cyanobacteria Mutant Strains and Processes for Phosphorus Recovery from Livestock Wastewater
    Brenda, Cansino-Loeza; Theodore A., Chavkin; Leonardo D., Gonzalez; Rebecca, Larson; Brian F., Pfleger; Victor M., Zavala
    Biological and Medicinal Chemistry on ChemRxiv
    2025-02-06
     The paper presents a cyanobacteria-based process for phosphorus recovery from livestock wastewater, achieving an 8.5-fold increase in biomass phosphorus density without affecting growth. Techno-economic modeling shows over a 2-fold reduction in total annualized costs and significant decreases in land use and energy. The combined process yields a phosphorus recovery charge of $9.2/kg, promoting a circular agricultural economy.

  • Nuclear Coupled Electronic States Analyses Expose Nuclear Quantum Effects in Nucleobase Pairs
    Hirotoshi , Mori; Kohei, Motoki
    Biological and Medicinal Chemistry on ChemRxiv
    2025-02-06
     The paper examines the nuclear quantum effects (NQEs) in the tautomerization of nucleobase pairs, specifically Cytosine-Guanine. Utilizing constrained nuclear-electronic orbital calculations, the study found that considering NQEs increased the probability of tautomer formation significantly—8.0 times in gas and 20.5 times in water. It estimates 246 tautomer pairs per human genome.

  • Power Series Representation of Reaction Rates in Chemical Kinetics and Its Physical Interpretation
    Jia, Qiu
    Theoretical and Computational Chemistry on ChemRxiv
    2025-02-07
     The paper presents a power series framework for modeling chemical reaction rates, enhancing traditional power-law models. It uses multivariate power series of reactant concentrations to account for multi-molecular interactions and synergistic effects, providing a more comprehensive understanding of reaction kinetics. The method offers improved mathematical flexibility and physical interpretation in representing reaction rates.

  • Fragment libraries from large synthetic compounds and natural products: A comparative chemoinformatic analysis
    José L., Medina-Franco; Verónica, Ramírez-Cid; Ana L., Chávez-Hernández; Osvaldo, Sánchez López; Raul, Marques Novais; Temitayo Omowumi, Alegbejo Price; Kamilla, Moraes Alves; Wemenes J., Lima Silva; Flavio da, Silva Emery; Carolina Horta, Andrade
    Theoretical and Computational Chemistry on ChemRxiv
    2025-02-06
     The paper presents a comparative analysis of fragment libraries derived from large natural product databases, specifically 2,583,127 fragments from COCONUT and 74,193 from LANaPDB, against the synthetic CRAFT library containing 1,214 fragments. The study assesses chemical space coverage and diversity, with the curated libraries available for public access.

  • Platinum-Modified Cantor Alloys as High-Entropy Electrocatalysts for Oxygen Reduction Reaction
    Christian Møgelberg, Clausen; Wiljar, Lobjakas; Jaak, Nerut; Jan, Rossmeisl
    Theoretical and Computational Chemistry on ChemRxiv
    2025-02-06
     The paper investigates platinum-modified Cantor alloys (CrCoFeMnNi) as high-entropy electrocatalysts for the oxygen reduction reaction (ORR). Using a machine learning-accelerated simulation protocol, the study identifies that Pt-rich alloys (approximately 80% Pt) exhibit the highest ORR activity due to synergistic effects. The findings advance the understanding of how bulk composition impacts kinetic behavior in complex alloys.

06 Feb 2025

  • Synthesis of Selectively 13C/2H/15N-Labelled Arginine to Probe Protein Conformation and Interaction by NMR Spectroscopy
    Paul Schanda, Darja Rohden, Giorgia Toscano, Roman Lichtenecker
    Organic Chemistry on ChemRxiv
    2025-02-05
     The paper presents a method for synthesizing selectively labeled arginine with 13C, 15N, and 2H isotopes to study protein conformation and interactions using NMR spectroscopy. This approach combines synthetic organic chemistry and protein overexpression, resulting in proteins with optimized NMR active spin systems that yield simplified spectra, enhancing sensitivity to environmental changes.

  • Designing reversible photoswitching azobenzene modified nucleotide for controlling biological function
    Ting Wang, Juncheng Li, Jinxi Du, Weiwei He, Ibrahim Adelakun, Miao Zhong, Savia Boyer, Ya Ying Zheng, Qishan Lin, Serdal Kirmizialtin, Jia Sheng
    Organic Chemistry on ChemRxiv
    2025-02-05
     The paper presents the design of a reversible photoswitchable azobenzene-modified nucleotide for controlling RNA functions. The authors synthesized modified RNA oligonucleotides and validated their reversible photoisomerization using all-atom molecular dynamics simulations and UV melting experiments. The modified oligonucleotides can influence reverse transcription processes upon light exposure, potentially aiding gene regulation and drug development.

  • Higher-level Strategies for Computer-Aided Retrosynthesis
    Jihye Roh, Joonyoung F. Joung, Kevin Yu, G. Logan Bartholomew, Omar A. Santiago-Reyes, Mun Hong Fong, Richmond Sarpong, Sarah E. Reisman, Connor W. Coley, Zhengkai Tu
    Organic Chemistry on ChemRxiv
    2025-02-05
     The paper presents a novel framework called higher-level retrosynthesis for computer-aided retrosynthesis, which simplifies complex synthetic pathways by emphasizing broader strategies rather than specific chemical details. The approach demonstrated higher success rates in both single- and multi-step planning through case studies on drugs and natural products, enhancing the effectiveness of synthesis design.

  • Enantioselective Synthesis of Complex Carbocycles by Donor/Donor Carbenes C-H insertion
    Jose Ruiz, Jared Shaw, Dylan Turner, Mingchun Gao, Wentao Guo, Tania Shahvali, Emily Jimenez Andrade, Beck Miller, Kevin Kong, James Fettinger, Matthew Sigman, Dean Tantillo
    Organic Chemistry on ChemRxiv
    2025-02-05
     The paper discusses the enantioselective synthesis of benzene-fused carbocycles through C–H insertion using rhodium donor/donor carbenes. The method shows chemoselectivity towards carbon centers with electron-donating heteroatoms. DFT calculations indicate a step-wise mechanism, shedding light on the stereoselectivity and preference for C–H over O–H insertion.

  • Fully-Functionalized Natural Product Probes to Expand the Chemical Tractability of the Human Proteome
    Christopher Parker, Christian Chaheine, Louis Conway
    Organic Chemistry on ChemRxiv
    2025-02-05
     The paper discusses the development of natural product-derived photoaffinity probes to enhance chemical proteomics for exploring the human proteome. The authors use mass spectrometry to identify unique ligand interactions in cells, demonstrating regio- and stereoselective binding for proteins lacking chemical probes. This approach could significantly expand the ligandable chemical space of the human proteome.

  • Visible-Light Photocatalysis Using CsPbX3 Perovskite Nanocrystals for Organic Transformations
    Prasenjit Mal, Pravat Nayek, Buddhadeb Pal
    Organic Chemistry on ChemRxiv
    2025-02-05
     The paper reviews the potential of CsPbX3 perovskite nanocrystals as photocatalysts for organic transformations, highlighting their unique properties and high solar radiation power conversion efficiency (up to 26.3%). It summarizes recent advancements, mechanistic insights, and future exploration opportunities in organic photocatalysis, emphasizing the relevance of these nanocrystals in improving synthetic methodologies.

  • On the Photosensitizing Properties of Aloe-Emodin in Photodynamic Therapy: Insights from the Molecular Modeling
    Maciej Spiegel
    Organic Chemistry on ChemRxiv
    2025-02-05
     The paper examines aloe-emodin’s photosensitizing properties using computational chemistry, revealing a 98:2 ratio of neutral to monoanionic species. Key findings include a two-photon absorption cross-section of 77 GM and triplet quantum yields of 0.51 and 0.79. The neutral form exhibits superior biomolecule oxidation and DNA intercalation, corroborating with experimental data.

  • Guanosine-based supramolecular particles for enhanced drug and gene delivery in cell culture
    Jose M. Rivera, Luis M. Negroán, Edwin Vázquez-Rosa, Luxene Belfleur, Tanya L. Díaz, Bismark Madera-Soto, Irving E. Vega
    Organic Chemistry on ChemRxiv
    2025-02-05
     The paper presents supramolecular hacky sacks (SHS), self-assembled particles from guanosine derivatives for drug and gene delivery. Confocal microscopy and flow cytometry show that SHS uptake depends on G-derivative composition. SHS effectively encapsulate doxorubicin and facilitate plasmid transfection, highlighting their biocompatibility and tunable bioactivity for biomedical applications.

  • The Hitchhiker’s Guide to Socratic Methods in Prompting Large Language Models for Chemistry Applications
    Hassan Harb, Yunkai Sun, Rajeev Surendran Assary
    Theoretical and Computational Chemistry on ChemRxiv
    2025-02-06
     The paper discusses the application of the Socratic method in prompting large language models (LLMs) for chemistry, focusing on iterative questioning to improve hypothesis refinement and problem-solving. It illustrates how integrating Socratic principles enhances LLM performance, adaptability, and model interpretability in scientific reasoning through examples from chemistry and materials research.

  • Refinement and Truncation of DNA Aptamers based on Molecular Dynamics Simulations: Computational Protocol and Experimental Validation
    Natalia Díaz, Ana Díaz-Fernández, Camen S. Ciudad, Dimas Suárez, Noemí de-los-Santos-Álvarez, M. Jesús Lobo-Castañón
    Theoretical and Computational Chemistry on ChemRxiv
    2025-02-05
     The paper presents a strategy for refining DNA aptamers using molecular dynamics simulations, which helps design shorter aptamers (20-35% shorter) with maintained or improved binding affinities. The protocol also assesses secondary structure stability and the impact of poly-thymine spacers. This method enhances optimization for aptamers used in diagnostics and therapeutic applications.

  • IR-Bot: an autonomous robotic system for real-time chemical mixture analysis via infrared spectroscopy and machine learning
    Linjiang Chen, Xiaoyu Yue, Tao Song, Jiaqi Cao, Xiaolong Zhang, Shuo Feng, Weiwei Shang, Jun Jiang
    Theoretical and Computational Chemistry on ChemRxiv
    2025-02-05
     The paper presents IR-Bot, an autonomous system for real-time chemical mixture analysis using infrared spectroscopy and machine learning. It employs a large-language-model-based IR Agent, multi-agent robotics, and a novel alignment-prediction approach to analyze binary and ternary mixtures. Results from a Suzuki coupling reaction demonstrate accurate predictions and insights into chemical behavior, enhancing data-driven laboratory workflows.

  • Pyrrolic FeN4 models for FeNC catalysts: the influence of planarity on electronic properties and Mӧssbauer parameters
    Niklas von Rhein, Jian Liang Low, Charlotte Gallenkamp, Beate Paulus, Vera Krewald
    Theoretical and Computational Chemistry on ChemRxiv
    2025-02-05
     The paper investigates the effects of planarity on electronic properties and Mӧssbauer parameters of pyrrolic FeN4 models in FeNC catalysts, alternative to platinum catalysts. It compares three pyrrolic models, focusing on the ability of spectroscopic techniques, especially Mӧssbauer spectroscopy, to detect differences in these models, which induce defects in the carbon matrix.

  • Atomic-Scale Observation of Moiré potential in Twisted Hexagonal Boron Nitride Layers by Electron Microscopy
    Takashi Uchino, Rina Mishima, Takuro Nagai, Hiroyo Segawa, Masahiro Ehara
    Theoretical and Computational Chemistry on ChemRxiv
    2025-02-05
     The paper presents a method for obtaining atomically clean twisted hexagonal boron nitride (hBN) layers to study moiré potentials via aberration-corrected electron microscopy. Using this technique, researchers observed moiré diffraction spots, enabling the reconstruction of moiré potential. Results indicate that local interlayer atomic overlap significantly influences the moiré potential’s periodicity and distribution, supported by density functional theory calculations.

05 Feb 2025

  • Machine learning-driven antiviral libraries targeting respiratory viruses
    José L. Medina-Franco, Gabriela Valle-Núñez, Raziel Cedillo-González, Juan F. Avellaneda-Tamayo, Fernanda I. Saldívar González, Diana L. Prado-Romero
    Biological and Medicinal Chemistry on ChemRxiv
    2025-02-04
     The paper explores the development of antiviral compound libraries targeting respiratory viruses using machine learning (ML) classification models. It created a curated dataset of compounds linked to respiratory infections, focusing on predicting antiviral activity. Validation of models was performed for seven respiratory targets, addressing the urgent need for new antiviral drugs highlighted by the SARS-CoV-2 pandemic.

  • Toward Far-red Emitting Chemogenetic Labelling for Live Cell Super-Resolution Microscopy using Fluorescence-Activating and Absorption-Shifting Tag
    Eszter Kozma, Ágnes Szatmári, Tibor Novák, György Török, Ivana Nikić-Spiegel, Attila Kormos, Gergely B. Cserép, Alexandra Egyed, Ágnes Horváth, Krisztina Németh, Réka Kereszty, Elvira Czvik, Miklós Erdélyi, Péter Kele
    Biological and Medicinal Chemistry on ChemRxiv
    2025-02-04
     The paper presents new chemogenetic approaches for far-red fluorescence detection in live cell super-resolution microscopy, using the Fluorescence-Activating and Absorption Shifting Tag (FAST). Methods include FRET-FAST for single molecule localization microscopy and a far-red variant (frFAST) for live imaging. Results demonstrate successful imaging of cytoskeletal dynamics and organelles without significant photobleaching in both fixed and live mammalian cells.

  • Fully-Functionalized Natural Product Probes to Expand the Chemical Tractability of the Human Proteome
    Christopher Parker, Christian Chaheine, Louis Conway
    Biological and Medicinal Chemistry on ChemRxiv
    2025-02-04
     The paper discusses the use of natural product-inspired photoaffinity probes to enhance chemical tractability of the human proteome. It employs semi-synthesis and mass spectrometry-based chemoproteomics to identify ligand interactions in human cells, revealing new regio- and stereoselective ligands for previously uncharacterized proteins. Results suggest these libraries significantly expand the ligandable proteome.

  • A Generalized Deep Entropy Scaling Architecture Framework to Predict Viscosities
    Maximilian Fleck, Niels Hansen, Timo Klenk, Samir Darouich, Marcelle B M Spera
    Theoretical and Computational Chemistry on ChemRxiv
    2025-02-04
     The paper presents a generalized deep learning framework for predicting viscosities, addressing data scarcity in sustainable material processes. It enhances a prior neural network model by removing specific entropy scaling dependencies. The model effectively predicts shear viscosities across diverse thermodynamic states and complex molecules, showing improved accuracy, ease of training, and versatile applications.

  • Multiple Molecule λ-Dynamics: Probing Drug Resistance with Concurrent Protein and Ligand Perturbations
    Jonah Vilseck, Ryan Hayes, Charles Brooks, Michael Liesen
    Theoretical and Computational Chemistry on ChemRxiv
    2025-02-04
     The paper presents Multiple Molecule λ-Dynamics (MMλD), a method for assessing drug resistance by simultaneously perturbing ligands and proteins in a single simulation. Applied to native and T315I mutant Abl kinases in chronic myelogenous leukemia, MMλD shows a high agreement with traditional methods, achieving mean unsigned errors of 0.21 and 0.79 kcal/mol, demonstrating its potential in drug discovery.

01 Feb 2025

  • Bayesian Illumination: Inference and Quality-Diversity Accelerate Generative Molecular Models
    Verhellen, Jonas
    Biological and Medicinal Chemistry on ChemRxiv
    2025-01-31
     The paper presents Bayesian Illumination, a novel generative model that integrates Bayesian optimization with a quality-diversity process for small molecules. It demonstrates that this approach outperforms traditional methods, such as genetic algorithms and deep learning, by generating a wider diversity of high-performing molecules and enhancing search efficiency. Key datasets include bespoke kernels for small molecules.

  • CRISPR in therapeutics and diagnostics: Perspectives from landscape analysis
    Iyer, Kavita; Tenchov, Rumiana; Diaz, Leilani Lotti; Jain, Preeti; Thite, Trupti; Deng, Yi; Zhou, Qiongqiong
    Biological and Medicinal Chemistry on ChemRxiv
    2025-01-31
     This paper analyzes over 53,000 publications on CRISPR therapeutics and diagnostics, revealing a focus on cancer and infectious diseases. Key gene targets include TP53, c-myc, and HBB, with adeno-associated vectors being a preferred delivery method. With over 140 CRISPR therapeutics in development, the field shows significant investment and growth despite ongoing ethical challenges.

  • Design, Synthesis and Preclinical Evaluation of a brain-permeable PET Tracer for P2Y12R Imaging in the Brain
    Lindner, Simon; Joseph, Emanuel; Kunze, Lea H.; Schaefer, Rebecca; Palumbo, Giovanna; Kugelmann, Benjamin; Wagner, Stephan; Lammich, Sven; Feederle, Regina; Willem, Michael; Werner, Rudolf A.; Brendel, Matthias
    Biological and Medicinal Chemistry on ChemRxiv
    2025-01-31
     The paper presents a novel brain-permeable PET tracer, Nicotinate [18F]12, designed for imaging P2Y12R-positive microglia, crucial for understanding neuroinflammation and neurodegenerative diseases. The tracer exhibited nanomolar affinity, with confirmed brain uptake in WT mice via PET imaging and ex vivo analyses, showing correlation with microglia activity. This advancement enhances diagnostic tools for treating microglial dysfunction.

  • Investigation of Arenes and Heteroarenes Nitration supported by High-Throughput Experimentation and Machine Learning
    Romero, Eugénie; Kerackian, Taline; Pasquinet, Eric; Daniel, Matthieu; Wespiser, Clément
    Organic Chemistry on ChemRxiv
    2025-01-31
     The paper explores the nitration of arenes and heteroarenes using high-throughput experimentation and machine learning. Diverse nitration conditions were systematically screened, generating significant data. Key trends related to electronic properties were identified, particularly the challenges with electron-poor heteroarenes. Machine learning was employed to design a predictive tool, highlighting the need for diverse and relevant data encoding.

  • Collective Intelligence of Specialized Language Models Guides Realization of de novo Chemical Synthesis
    Li, Haote; Sarkar, Sumon; Lu, Wenxin; Loftus, Patrick; Qiu, Tianyin; Shee, Yu; Cuomo, Abbigayle; Webster, John-Paul; Kelly, H. Ray; Manee, Vidhyadhar; Sreekumar, Sanil; Buono, Frederic; Crabtree, Robert; Newhouse, Timothy; Batista, Victor
    Organic Chemistry on ChemRxiv
    2025-01-31
     The paper introduces MOSAIC, a framework using Llama3.1-8B-instruct architecture and 2,489 specialized models to analyze chemical reactions effectively. It predicts novel transformations, successfully synthesizing over 35 new compounds from diverse categories. This approach enhances the utilization of existing chemical knowledge, fostering advancements in computational and experimental chemistry.

  • Knowledge-informed molecular design for zeolite synthesis using ChatGPT towards human-machine collaboration
    Muraoka, Koki; Ito, Shusuke; Nakayama, Akira
    Organic Chemistry on ChemRxiv
    2025-01-31
     The paper discusses leveraging Large Language Models (LLMs) for designing organic structure-directing agents (OSDAs) for zeolites. The method combines LLM-generated proposals with empirical feedback and atomistic simulations, resulting in candidates that enhance predictability and exploration of chemical space. The outcomes include validated and novel OSDAs with improved affinity scores, highlighting the potential of human-machine collaboration in molecular design.

  • Molecular Simulations with a Pretrained Neural Network and Universal Pairwise Force Fields
    Kabylda, Adil; Frank, J. Thorben; Dou, Sergio Suarez; Khabibrakhmanov, Almaz; Sandonas, Leonardo Medrano; Unke, Oliver T.; Chmiela, Stefan; Müller, Klaus-Robert; Tkatchenko, Alexandre
    Theoretical and Computational Chemistry on ChemRxiv
    2025-01-31
     The paper presents the SO3LR method, combining the SO3krates neural network with universal pairwise force fields, trained on 4 million molecular complexes. It achieves efficiency, scalability, and accuracy in molecular simulations, applicable to various biomolecules and large systems. The study highlights computational benefits and addresses future challenges in integrating MLFFs with atomistic models.

31 Jan 2025

  • Identifying organic co-solvents via machine learning solubility predictions in organic solvents and water
    Maurycy, Krzyzanowski; Sirazam Munira, Aishee; Nirala, Singh; Bryan R., Goldsmith
    Organic Chemistry on ChemRxiv
    2025-01-30
     The paper develops a machine learning workflow to identify effective organic co-solvents for increasing the solubility of hydrophobic molecules in water. Using the AqSolDB and BigSolDB datasets, it employs a Light Gradient Boosting Machine model, achieving R2 scores of 0.864 for aqueous and 0.805 for organic solubility. The model’s predictions are validated experimentally with benzaldehyde and limonene.

  • Multiple Atropo Selectivity by κ2-N,O-Oxazoline Urea Ligands in Cobaltaelectro-Catalyzed C–H Activations: Decoding Selectivity with Data Science Integration
    Neeraj Kumar, Pandit; Philipp, Boos; Suman, Dana; Tristan, von Münchow; Airu, Hashidoko; Laura, Haberstock; Regine, Herbst-Irmer; Dietmar, Stalke; Lutz, Ackermann
    Organic Chemistry on ChemRxiv
    2025-01-30
     The paper presents a new class of chiral oxazoline urea ligands for enantioselective catalysis, evaluated against amide and enol derivatives. A multivariate linear regression model was developed to analyze the impact of ligand and substrate structures on enantioselectivity, applied in cobaltaelectro-catalyzed C–H annulations of 1-alkynyl indoles, enhancing understanding of selectivity in these reactions.

  • Rapid photoluminescence “turn-on” sensing of tertiary amines and opioids via dual-emissive ground and excited charge-transfer states
    Aoyuan, Cheng; Xuewen, Gu; Chengze, Yang; Mei, Liu; Baicheng, Zhang; Hongping, Liu; Xiaoyu, Chen; Airong, Feng; Jun, Jiang; Yi, Luo; Pieter E. S., Smith; Wenhuan, Huang; Guoqing, Zhang
    Organic Chemistry on ChemRxiv
    2025-01-30
     The paper presents a novel photoluminescence “turn-on” method for distinguishing tertiary amines using naphthalimide, showcasing varying emission colors based on molecular structure. This approach effectively identifies opioids like heroin and fentanyl, offering a rapid alternative to traditional methods. The study highlights unique excited-state dynamics and includes observations from time-resolved spectroscopy.

  • Uracil-BX: A New Class of Cyclic Hypervalent Iodine Reagents for Unraveling Approach Towards Umpolung Functionalization and VEGF G-Quadruplex DNA Identification
    Raj Kumar, Nandi; Sukanya, Das; Sagar, Bag; Md Abbasuddin, Sk; Priyankar, Majumdar; Uttam Kumar, Das; Sudipta, Bhowmik
    Organic Chemistry on ChemRxiv
    2025-01-30
     The paper introduces Uracil-BX, a novel cyclic hypervalent iodine reagent designed for umpolung functionalization and G-Quadruplex DNA identification. It describes synthetic methods for sulfenylation and amination, and highlights compound UBX 3a’s interactions with VEGF GQ-DNA, which may influence cancer gene expression and aid future GQ biology research. Biophysical studies support these findings.

  • The Chemistry and Biology of the Tetrodotoxin Natural Product Family
    David, Konrad; Benedikt, Nißl; Marcel, Mülbaier; Francesca, Grisoni; Dirk, Trauner; Marcel, Bermúdez; Clemens, Dialer
    Organic Chemistry on ChemRxiv
    2025-01-30
     The paper reviews tetrodotoxin, a neurotoxic marine alkaloid, discussing its structural complexities, biological activities, and potential therapeutic applications. It covers the diversity of its natural derivatives, biosynthetic pathways, and structure-activity relationships, along with total syntheses reported so far. No specific datasets or methods were mentioned in the abstract.

  • Chiral Phosphite Mediated Photoredox Catalyzed Aerobic Oxidative DYKAT for C–N Atropoisomers
    Pradip, Maity; Pinku, Saikia; M, Aarthika; Ayantika, Bhattacharjya; Priyam, Bajpai; Susmita, Maity; Asish, Bera; Arindam, Saha; Rajesh, Gonnade; Kumar, Vanka
    Organic Chemistry on ChemRxiv
    2025-01-30
     The paper presents a novel phosphite-mediated method for atroposelective synthesis of C–N atropoisomers via Dynamic Kinetic Asymmetric Transformation (DYKAT). The approach effectively oxidizes iminium ions, allowing a broader range of substrates including isoquinolones, pyridones, and lactams. Computational studies back the mechanism, offering a new strategy that enhances diversity in synthesizing axially chiral compounds.

30 Jan 2025

  • Rivers at Risk: A Comprehensive Review of Human-Induced Pollution and Its Seasonal Variation
    Mitasha, Kaushik; Manish, Sharma
    Organic Chemistry on ChemRxiv
    2025-01-29
     The paper reviews human-induced pollution in rivers, focusing on India and China, with a dataset encompassing water quality tests from 603 rivers. It employs multivariate statistical methods to analyze seasonal variations, finding that 90% of water samples in Uttarakhand were contaminated. Key analyzed parameters included TDS, BOD, and E. coli. The study calls for coordinated global efforts to tackle the water crisis.
  • Discovery of Clonixeril as a Sub-Femtomolar Modulator of the Human STING Receptor
    Wayne, Guida; Robert, Sparks; William, Lawless; Sarah, Lawless; Mark, Eschenfelder; Rainer, Metcalf; Kenyon, Daniel; Anna, Kharitonova; Grace, Binder; Jamie, Nunziata; Sauradip, Chaudhury; Christine, Gambino; Michelle, Wilde; Donna, Trask; Linette, Harding; Jaret, Crews; Mansi, Gopu; Emilia, Dalamangus; Robert, Green; Elizabeth, Nompleggi; Paul, Thompson; Niketa, Patel; Rekha, Patel; Guy, Bradley; Wesley, Brooks; Mildred, Acevedo-Duncan; Alan, Mullen; James, Leahy; Timothy, Tran; Yan, Yang
    Organic Chemistry on ChemRxiv
    2025-01-29
     The paper reports the discovery of clonixeril (CXL) as a potent modulator of the human STING receptor, with an EC50 ranging from 1 fM to above 1 nM based on in vitro and in cellulo studies. Molecular dynamics models and biophysical techniques were employed for characterization, revealing CXL’s strong inhibitory effect on interferon production in THP-1 cells.
  • Expediting hit-to-lead progression in drug discovery through reaction prediction and multi-objective molecular optimization
    Kenneth, Atz; David F., Nippa; Yannick, Stenzhorn; Alex T., Müller; Andreas, Tosstorff; Jörg, Benz; Hayley, Binch; Markus, Bürkler; Achi, Haider; Dominik, Heer; Remo, Hochstrasser; Christian, Kramer; Michael, Reutlinger; Petra, Schneider; Thierry, Shema; Andreas, Topp; Alexander, Walter; Matthias B., Wittwer; Jens, Wolfard; Bernd, Kuhn; Mario, van der Stelt; Rainer E., Martin; Uwe, Grether; Gisbert, Schneider
    Organic Chemistry on ChemRxiv
    2025-01-29
     The paper presents an integrated medicinal chemistry workflow that accelerates hit-to-lead optimization in drug discovery. Using high-throughput experimentation, a dataset of 13,490 reaction outcomes was generated, training deep graph neural networks. A virtual library of 26,375 molecules led to 212 candidate MAGL inhibitors, with 14 achieving subnanomolar activity, improving potency up to 4500 times over original compounds.
  • Quaternary biopesticides and disinfectants derived from quinine and amino acids – environmental prospects and risks
    Tomasz, Rzemieniecki; Krzysztof, Juś; Tomasz, Klejdysz; Daniela, Gwiazdowska
    Organic Chemistry on ChemRxiv
    2025-01-29
     The paper explores new, safer quaternary ammonium salts (QASs) synthesized from quinine and amino acids, specifically L-asparagine and L-alanine. Characterized for chemical structure and biological activity, these compounds show strong antifeedant effects and low phytotoxicity. Toxicity assessments on various organisms (Sorghum bicolor, Sinapis alba, Chlorella vulgaris, Daphnia magna) reveal promising environmental safety for these biopesticides.
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