Hasil untuk "Organic chemistry"

Mohamad Koohi-Moghadam, Hongzhe Sun, Hongyan Li et al.

The discovery of anticancer therapeutics has traditionally treated organic small molecules and metal-based coordination complexes as separate chemical domains, limiting knowledge transfer despite their shared biological objectives. This disparity is particularly pronounced in available data, with extensive screening databases for organic compounds compared to only a few thousand characterized metal complexes. Here, we introduce ChemCLIP, a dual-encoder contrastive learning framework that bridges this organic-inorganic divide by learning unified representations based on shared anticancer activities rather than structural similarity. We compiled complementary datasets comprising 44,854 unique organic compounds and 5,164 unique metal complexes, standardized across 60 cancer cell lines. By training parallel encoders with activity-aware hard negative mining, we mapped structurally distinct compounds into a shared 256-dimensional embedding space where biologically similar compounds cluster together regardless of chemical class. We systematically evaluated four molecular encoding strategies: Morgan fingerprints, ChemBERTa, MolFormer, and Chemprop, through quantitative alignment metrics, embedding visualizations, and downstream classification tasks. Morgan fingerprints achieved superior performance with an average alignment ratio of 0.899 and downstream classification AUCs of 0.859 (inorganic) and 0.817 (organic). This work establishes contrastive learning as an effective strategy for unifying disparate chemical domains and provides empirical guidance for encoder selection in multi-modal chemistry applications, with implications extending beyond anticancer drug discovery to any scenario requiring cross-domain chemical knowledge transfer.

Qingqiang Tian, Chuxia Wang, Bingrui Liu et al.

Abstract α−Sulfide disulfides represent valuable motifs in organic and pharmaceutical chemistry. However, the limited availability of synthetic approaches for α−sulfide disulfides has impeded progress in this field. In this study, a photocatalytic approach to synthesizing modifiable α−sulfide disulfides is presented using accessible sulfides and a bilateral disulfurating reagent. The reaction proceeds under mild conditions and demonstrates broad substrate compatibility, accommodating both aromatic and aliphatic sulfides. Moreover, the synthesized α−sulfide disulfides display robust reactivity in subsequent transformations with different electrophiles. Notably, this protocol can also be applied to the modification of polymer matrices. Bioassays further reveal that certain target compounds exhibit significant antibacterial activity against plant pathogens, such as Xanthomonas oryzae pv. oryzae (Xoo), Xanthomonas oryzae pathovar oryzicola (Xoc), and Dickeya zeae (D. zeae).

Muhammad Mazher Irshad , Kausar Noor, Muhammad Imran Khan et al.

Background: Laparoscopic surgery is increasingly preferred for various abdominal procedures due to its minimally invasive nature. However, port site complications, particularly wound infections, remain a significant concern. The method of umbilical access—either intra-umbilical or periumbilical—may influence the rate of postoperative infections, yet evidence comparing the two remains limited. The study aimed to compare the frequency of wound infection between intra-umbilical and periumbilical incisions in patients undergoing laparoscopic appendectomy or cholecystectomy. Methods: A descriptive study was conducted over six months in the Department of Surgery at Khyber Teaching Hospital, Peshawar. A total of 201 patients undergoing laparoscopic surgeries were enrolled using a non-probability consecutive sampling technique. Patients were divided into Group A (intra-umbilical incision, n=101) and Group B (periumbilical incision, n=100). Baseline demographics, comorbidities, and type of surgery were recorded. Postoperative wound infections were assessed within two weeks based on predefined clinical criteria. Data were analyzed using SPSS v25, with Chi-square and Fisher's exact tests applied where appropriate. Results: The overall wound infection rate was 11.4%, with 8 infections (7.9%) in Group A and 15 infections (15%) in Group B. The infection rate was nearly double in the periumbilical group compared to the intra-umbilical group. Other variables, including comorbidities and type of surgery, were comparable between the groups. Conclusion: Intra-umbilical incisions were associated with a lower incidence of wound infections compared to periumbilical incisions in laparoscopic procedures. This method may offer a safer and cosmetically superior alternative for initial port access in routine laparoscopic surgeries 

Rachel E. Gross, L. Ilsedore Cleeves

The chemistry within a protoplanetary disk is greatly affected by external radiation from the local stellar environment. Previous work has focused on extreme radiation fields, representative of the center of something like the Orion Nebula Cluster. However, even in such environments, many disks exist at the edges of a cluster where the lower stellar density leads to radiation fields weaker by orders of magnitude compared to the center. We present new chemical models of a T-Tauri disk in the presence of a moderately increased interstellar radiation field (ISRF). Such an environment has a background UV strength of 10 to 100 times higher than the galactic average ISRF. Moderate radiation fields are among the most prevalent disk-harboring environments and have interesting implications for the chemistry of the outer disk radii. We find that the external UV radiation creates an outer ionization front that impacts the cold disk chemistry to varying degrees, depending on outer disk structure. Certain molecules like C$^+$, N$_2$H$^+$, C, and CS are more strongly impacted by the ISRF in their abundance, column density, and observable emission. Other abundant species like HCO$^+$ and CO are less affected by the external UV flux in the outer disk under such moderate UV conditions. Further, we demonstrate that the chemistry occurring in the inner tens of au is relatively unchanged, which suggests that even in moderately externally irradiated disks, the inner disk chemistry may be more similar to isolated disks like those in, e.g., the Taurus and Lupus star-forming regions.

Zhihao Zhang, Xiao-Ming Cao

Deep learning has advanced efficient chemical process simulations on the surfaces, accelerating high-throughput materials screening and rational design in heterogeneous catalysis, energy storage and conversion, and gas separation. However, the accuracy of the deep learning model generally depends on the quality of the training data. Unfortunately, precise experimental data in surface chemistry, such as adsorption energies, are scarce, while accurate quantum chemistry simulations remain computationally prohibitive for large-scale studies. Herein, we present a deep learning model of DOS Transformer for Adsorption (DOTA) for efficient surface chemistry simulations with chemical accuracy. It enables the alignment of experimental data and multi-fidelity quantum chemistry calculation data by capturing latent orbital interaction patterns based on the map between local density of states (LDOS) and adsorption energy. This minimizes the reliance on scarce high-precision training data in surface chemistry to accomplish efficient prediction of adsorption energies rivaling the high-precision experimental data, resolving the long-standing challenge of "CO puzzle". It provides a robust framework for efficient materials screening, effectively bridging the gap between computational and experimental data.

Siddharth M. Narayanan, James D. Braza, Ryan-Rhys Griffiths et al.

Reasoning models are large language models that emit a long chain-of-thought before answering, providing both higher accuracy and explicit reasoning for their response. A major question has been whether language model reasoning generalizes beyond mathematics, programming, and logic, where most previous work has focused. We demonstrate that reasoning models can be post-trained for chemistry without additional domain pretraining, and require substantially less data compared to contemporary domain-specific models. We report ether0, a 24B parameter LLM (based on Mistral-Small-24B) that can reason in natural language and respond with chemical structures. This reasoning model was trained with reinforcement learning on 640,730 experimentally-grounded chemistry problems across 375 tasks ranging from synthesizability, to blood-brain barrier permeability, to human receptor activity, to scent. Our model exceeds general-purpose chemistry models, frontier models, and human experts on molecular design tasks. It is also more data efficient relative to specialized models. We anticipate that this method can be applied to train data-efficient language models specialized for tasks across a wide variety of scientific domains.

Shantanu Mishra, Valentina Malave, Rasmus Svensson et al.

Skeletal editing of cyclic molecules has garnered considerable attention in the context of drug discovery and green chemistry, with notable examples in solution-phase synthesis. Here, we extend the scope of skeletal editing to the single-molecule scale. We demonstrate tip-induced oxygen deletion and ring contraction of an oxygen-containing seven-membered ring on bilayer NaCl films to generate molecules containing the perylene skeleton. The products were identified and characterized by atomic force and scanning tunneling microscopies, which provided access to bond-resolved molecular structures and orbital densities. Insights into the reaction mechanisms were obtained by density functional theory calculations. Our work expands the toolbox of tip-induced chemistry for single-molecule synthesis.

Antonio D’Errico, Rosarita Nasso, Rosario Rullo et al.

Monoamine oxidase and xanthine oxidase inhibitors represent useful multi-target drugs for the prevention, attenuation, and treatment of oxidative damage and neurodegenerative disorders. Chimeric molecules, constituted by naturally derived compounds linked to drugs, represent lead compounds to be explored for the discovery of new synthetic drugs acting as enzyme inhibitors. We have previously reported that seven hydroxytyrosol-donepezil hybrid compounds play a protective role in an in vitro neuronal cell model of Alzheimer’s disease. In this work, we analyzed the effects exerted by the hybrid compounds on the activity of monoamine oxidase A (MAO-A) and B (MAO-B), as well as on xanthine oxidase (XO), enzymes involved in both neurodegenerative disorders and oxidative stress. The results pointed to the identification, among the compounds tested, of selective inhibitors between the two classes of enzymes. While the 4-hydroxy-3-methoxyphenethyl 1-benzylpiperidine-4-carboxylate- (HT3) and the 4-hydroxyphenethyl 1-benzylpiperidine-4-carboxylate- donepezil derivatives (HT4) represented the best inhibitors of MAO-A, with a scarce effect on MAO-B, they were almost ineffective on XO. On the other hand, the 4,5-dihydroxy-2-nitrophenethyl 1-benzylpiperidine-4-carboxylate donepezil derivative (HT2), the least efficient MAO inhibitor, acted like the best XO inhibitor. Therefore, the differential enzymatic targets identified among the hybrid compounds synthesized enhance the possible applications of these polyphenol-donepezil hybrids in neurodegenerative disorders and oxidative stress.

Robert P. Crease, Vladimir Shiltsev

This article, the third in a series about the Russian scientist Mikhail Lomonosov (1711-1765), covers the first decade of his research at the St. Petersburg Academy of Sciences, from his return from an educational his trip abroad in 1741, to the mid-1750s. Lomonosov's major focus was on the establishment of the first Russian laboratory used to introduce modern experimental chemistry and physics methods both to original research and education. The lab supported studies of the physics of colors, chemistry and physics of glasses and training of the Academy students. This article describes how Lomonosov, first an Adjunct Professor and then as a young Professor, fought to create the chemistry lab, and then to establish a broad program of experiments and tests there. The construction of laboratories to be used not just for research but also education only became widespread in the early 19th century, but Lomonosov's laboratory had a significant impact on the early development of the Academy and on Russian science.

Katerina P. Hilleke, Eva Zurek

An overview of the behavior of materials at high pressure is presented, starting from the effects on single atoms driving electronic transitions and changes in periodic trends. A range of high-pressure-induced phenomena in the solid state are then discussed building on the atomic changes, including bizarre electronic structures, electrides, compounds of noble gases, changes in elemental miscibility, and strange structural and bonding configurations. In the final section, the field of high pressure superconductivity is discussed, as high pressure phases have generated immense study and excitement as some of their critical superconducting temperatures approach room temperature.

Haibao Lu

Can the laws of physics be unified. One of the most puzzling challenges is to reconcile physics and chemistry, where molecular physics meets condensed-matter physics, resulting from the scaling effect and dynamic fluctuation of glassy matter at the glass transition temperature. Pioneer of condensed-matter physics, the Nobel Prize-winning physicist Philip Warren Anderson, wrote in 1995: The deepest and most interesting unsolved problem in condensed-matter physics is probably the theory of the nature of glassy state and the glass transition. In 2005, the question of 'what is the nature of glassy state' was suggested as one of the greatest scientific conundrums over the next quarter-century for Science's 125th anniversary. However, the nature of glassy state and its connection to the glass transition have not been fully understood owing to the interdisciplinary complexity of physics and chemistry, where they are governed by the physical laws at condensed-matter and molecular scales, respectively. Therefore, study on the glass transition becomes essential to explore the working principles of scaling effect and dynamic fluctuation in glassy matter, as well as further reconcile the interdisciplinary complexity of physics and chemistry.

Lisa Schmidt, Danny Wagner, Martin Nieger et al.

A series of <i>C</i>₃-symmetric fully substituted benzenes were prepared based on alkyl triamino-benzene-tricarboxylates. Starting with a one step-synthesis, the alkyl triamino-benzene-tricarboxylates were synthesized using the corresponding cyanoacetates. The reactivity of these electronically sophisticated compounds was investigated by the formation of azides, the click reaction of the azides and a <span style="font-variant: small-caps;">Sandmeyer</span>-like reaction. Caused by the low stability of triaminobenzenes, direct <i>N</i>-alkylation was rarely reported. The use of the stable alkyl triamino-benzene-tricarboxylates allowed us total <i>N</i>-alkylation under standard alkylation conditions. The molecular structures of the <i>C</i>₃-symmetric structures have been corroborated by an X-ray analysis.

Si-Li He, Ya-Ling Chen, Qi-Hua Chen et al.

Highlights 1. LncRNA KCNQ1OT1 is upregulated, while EIF2B5 is downregulated in OC tissues and cells. 2. Knockdown of KCNQ1OT1 represses OC cell proliferation and metastasis. 3. KCNQ1OT1 decreases EIF2B5 expression by recruiting DNA methyltransferases into EIF2B5 promoter, thereby promoting OC progression.

Zoi Terzopoulou, Eleftheria Xanthopoulou, Nikolaos Pardalis et al.

Lignin, being one of the main structural components of lignocellulosic biomass, is considered the most abundant natural source of phenolics and aromatics. Efforts for its valorisation were recently explored as it is mostly treated as waste from heat/energy production via combustion. Among them, polymer-based lignin composites are a promising approach to both valorise lignin and to fine tune the properties of polymers. In this work, organosolv lignin, from beech wood, was used as fillers in a poly (lactic acid) (PLA) matrix. The PLA/lignin composites were prepared using melt mixing of masterbatches with neat PLA in three different lignin contents: 0.5, 1.0 and 2.5 wt%. Lignin was used as-isolated, via the organosolv biomass pretreatment/fractionation process and after 8 h of ball milling. The composites were characterised with Scanning Electron Microscopy (SEM), Fourier Transform Infrared Spectroscopy (FTIR) spectroscopy, X-ray Diffraction (XRD), and Differential Scanning Calorimetry (DSC). Additionally, their antioxidant activity was assessed with the 2,2-Diphenyil-1-picrylhydrazyl (DPPH) method, the colour was measured with a colorimeter and the mechanical properties were evaluated with tensile testing. Ball milling, at least under the conditions applied in this study, did not induce a further substantial decrease in the already relatively small organosolv lignin primary particles of ~1 μm. All the produced PLA/lignin composites had a uniform dispersion of lignin. Compression-moulded films were successfully prepared, and they were coloured brown, with ball-milled lignin, giving a slightly lighter colour in comparison with the as-received lignin. Hydrogen bonding was detected between the components of the composites, and crystallization of the PLA was suppressed by both lignin, with the suppression being less pronounced by the ball-milled lignin. All composites showed a significantly improved antioxidant activity, and their mechanical properties were maintained for filler content 1 wt%.

Mihaela Savin, Carmen-Marinela Mihailescu, Carmen Moldovan et al.

Nanocomposite materials have seen increased adoption in a wide range of applications, with toxic gas detection, such as carbon monoxide (CO), being of particular interest for this review. Such sensors are usually characterized by the presence of CO absorption sites in their structures, with the Langmuir reaction model offering a good description of the reaction mechanism involved in capturing the gas. Among the reviewed sensors, those that combined polymers with carbonaceous materials showed improvements in their analytical parameters such as increased sensitivities, wider dynamic ranges, and faster response times. Moreover, it was observed that the CO reaction mechanism can differ when measured in mixtures with other gases as opposed to when it is detected in isolation, which leads to lower sensitivities to the target gas. To better understand such changes, we offer a complete description of carbon nanostructure-based chemosensors for the detection of CO from the sensing mechanism of each material to the water solution strategies for the composite nanomaterials and the choice of morphology for enhancing a layers’ conductivity. Then, a series of state-of-the-art resistive chemosensors that make use of nanocomposite materials is analyzed, with performance being assessed based on their detection range and sensitivity.

Ahmad Peyvan, Khemraj Shukla, Jesse Chan et al.

We compare high-order methods including spectral difference (SD), flux reconstruction (FR), the entropy-stable discontinuous Galerkin spectral element method (ES-DGSEM), modal discontinuous Galerkin methods, and WENO to select the best candidate to simulate strong shock waves characteristic of hypersonic flows. We consider several benchmarks, including the Leblanc and modified shock-density wave interaction problems that require robust stabilization and positivity-preserving properties for a successful flow realization. We also perform simulations of the three-species Sod problem with simplified chemistry with the chemical reaction source terms introduced in the Euler equations. The ES-DGSEM scheme exhibits the highest stability, negligible numerical oscillations, and requires the least computational effort in resolving reactive flow regimes with strong shock waves. Therefore, we extend the ES-DGSEM to hypersonic Euler equations by deriving a new set of two-point entropy conservative fluxes for a five-species gas model. Stabilization for capturing strong shock waves occurs by blending high-order entropy conservative fluxes with low-order finite volume fluxes constructed using the HLLC Riemann solver. The hypersonic Euler solver is verified using the non-equilibrium chemistry Sod problem. To this end, we adopt the Mutation++ library to compute the reaction source terms, thermodynamic properties, and transport coefficients. We also investigate the effect of real chemistry versus ideal chemistry, and the results demonstrate that the ideal chemistry assumption fails at high temperatures, hence real chemistry must be employed for accurate predictions. Finally, we consider a viscous hypersonic flow problem to verify the transport coefficients and reaction source terms determined by the Mutation++ library.

N. Carrasco, J. Bourgalais, L. Vettier et al.

Context. The chemical building blocks of life contain a large proportion of nitrogen, an essential element. Titan, the largest moon of Saturn, with its dense atmosphere of molecular nitrogen and methane, offers an exceptional opportunity to explore how this element is incorporated into carbon chains through atmospheric chemistry in our Solar System. A brownish dense haze is consistently produced in the atmosphere and accumulates on the surface on the moon. This solid material is nitrogen-rich and may contain prebiotic molecules carrying nitrogen. Aims. To date, our knowledge of the processes leading to the incorporation of nitrogen into organic chains has been rather limited. In the present work, we investigate the formation of nitrogen-bearing ions in an experiment simulating Titan s upper atmosphere, with strong implications for the incorporation of nitrogen into organic matter on Titan. Methods. By combining experiments and theoretical calculations, we show that the abundant N2+ ion, produced at high altitude by extreme-ultraviolet solar radiation, is able to form nitrogen-rich organic species. Results. An unexpected and important formation of CH3N2+ and CH2N2+ diazo-ions is experimentally observed when exposing a gas mixture composed of molecular nitrogen and methane to extreme-ultraviolet radiation. Our theoretical calculations show that these diazo-ions are mainly produced by the reaction of N2+ with CH3 radicals. These small nitrogen-rich diazo-ions, with a N/C ratio of two, appear to be a missing link that could explain the high nitrogen content in Titan s organic matter. More generally, this work highlights the importance of reactions between ions and radicals, which have rarely been studied thus far, opening up new perspectives in astrochemistry.

Aditi S. Krishnapriyan, Joseph Montoya, Maciej Haranczyk et al.

Abstract Machine learning has emerged as a powerful approach in materials discovery. Its major challenge is selecting features that create interpretable representations of materials, useful across multiple prediction tasks. We introduce an end-to-end machine learning model that automatically generates descriptors that capture a complex representation of a material’s structure and chemistry. This approach builds on computational topology techniques (namely, persistent homology) and word embeddings from natural language processing. It automatically encapsulates geometric and chemical information directly from the material system. We demonstrate our approach on multiple nanoporous metal–organic framework datasets by predicting methane and carbon dioxide adsorption across different conditions. Our results show considerable improvement in both accuracy and transferability across targets compared to models constructed from the commonly-used, manually-curated features, consistently achieving an average 25–30% decrease in root-mean-squared-deviation and an average increase of 40–50% in R2 scores. A key advantage of our approach is interpretability: Our model identifies the pores that correlate best to adsorption at different pressures, which contributes to understanding atomic-level structure–property relationships for materials design.

Shidong Song, Alexander F. Mason, Richard A. J. Post et al.

Weronika Mucha, Dorota Witkowska

Essential oils (EOs) have been used for centuries, and interest in these compounds has been revived in recent years. Due to their unique chemical composition as well as antimicrobial, immunostimulatory, anti-inflammatory and antioxidant properties, EOs are used in pharmacology, cosmetology and, increasingly, in animal breeding and rearing, and processing of animal raw materials. Essential oils have become a natural alternative to preservatives, taste enhancers and, most importantly, antibiotics, because the European Union banned the use of antibiotics in metaphylaxis in animal husbandry in 2006. In the animal production chain, EOs are used mainly as feed additives to improve feed palatability and increase feed intake, improve animal resistance and health status, and to prevent and treat diseases. Recent research indicates that EOs can also be applied to sanitize poultry houses, and they can be used as biopesticides in organic farming. Essential oils effectively preserve meat and milk and, consequently, improve the safety, hygiene and quality of animal-based foods. Novel technologies such as encapsulation may increase the bioavailability of EOs and their application in the production of food and feed additives.