jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Paul A. Johnson | Charles‐Émile Fecteau | Samuel Nadeau | Mauricio Rodríguez‐Mayorga | Pierre‐François Loos
Source: ArXiv.org (preprint, 2025-10-07)
Field: Chemistry — Spectroscopy

Connections between Richardson-Gaudin States, Perfect-Pairing, and Pair Coupled-Cluster Theory Slater determinants underpin most electronic structure methods, but orbital-based approaches often struggle to describe strong correlation efficiently. Geminal-based theories, by contrast, naturally capture static correlation in bond-breaking and multireference problems, though at the expense of implementation complexity and limited treatment of dynamic effects. In this work, we examine the interplay between orbital and geminal frameworks, focusing on perfect-pairing (PP) wavefunctions and their relation to pair coupled-cluster doubles (pCCD) and Richardson-Gaudin (RG) states. We show that PP arises as an eigenvector of a simplified reduced Bardeen-Cooper-Schrieffer (BCS) Hamiltonian expressed in bonding/antibonding orbital pairs, with the complementary eigenvectors enabling a systematic treatment of weak correlation. Second-order Epstein-Nesbet perturbation theory on top of PP is found to yield energies nearly equivalent to pCCD. These results clarify the role of pair-based ansätze and open avenues for hybrid approaches that combine the strengths of orbital- and geminal-based methods. Geminal ; Wave function ; Hamiltonian (control theory) ; Eigenvalues and eigenvectors ; Perturbation theory (quantum mechanics) ; Perturbation (astronomy) Molecular spectroscopy and chirality ; Algebraic structures and combinatorial models ; Magnetism in coordination complexes
Authors: Temel Kan Bakır | Halit Muğlu
Source: Bitlis Eren Üniversitesi Fen Bilimleri Dergisi (article, 2025-09-30)
Field: Chemistry — Organic Chemistry

Synthesis, Spectroscopic Studies and Antioxidant Activities of New 2-Benzylidene-N-Phenylhydrazine-1-Carbothioamide Derivatives Nowadays, thiosemicarbazone based schiff bases, which are the focus of attention due to their differential properties, are being synthesized in many studies and new aromatic structure added compounds are of significant interest in drug design and biochemistry. In this study, new thiosemicarbazide schiff bases containing different substituted groups were synthesized. The structure of new compound derivatives was characterized by proton nuclear magnetic resonance (1H-NMR), carbon-13 nuclear magnetic resonance (13C-NMR), fourier transform infrared spectroscopy (FTIR) and elemental analyses. In addition, radical quenching capacities of newly synthesized compounds were investigated using 1,1-diphenyl-2-picryl hydrazyl (DPPH) method. IC50 values were calculated for the compounds and it was found that the antioxidant activities of the compounds changed in the order of 2&gt;5&gt;1&gt;4&gt;3. These results indicated that the presence of methoxy substituted groups that provide electrons to the aromatic ring structures of schiff bases would have positive effects on the antioxidant activities of the compounds. Antioxidant ; Ring (chemistry) ; Schiff base ; Fourier transform infrared spectroscopy ; Semicarbazone ; Infrared spectroscopy ; Quenching (fluorescence) ; Proton NMR ; Electron paramagnetic resonance Synthesis and biological activity ; Free Radicals and Antioxidants ; Metal complexes synthesis and properties
Authors: Xingxing Li | Nan Song | Wenyao Chen | Junbo Cao | Jing Zhang | Xinggui Zhou | De Chen | Xuezhi Duan
Source: Nano Research (article, 2025-05-29)
Field: Materials Science — Materials Chemistry

Regulation of micro-environments by multi-metal promoters: A theoretical study on CO <sub>2</sub> activation over iron carbide catalysts Essentially developing and regulating the unique electronic property of iron carbide catalysts involving multi-metal promoters to understand the structure-activity relationship of the CO<sub>2</sub> activation process is still a great challenge. Here, metals and transition metals were introduced as strategies for electronic structure regulation to theoretically understand the underlying nature of CO<sub>2</sub> adsorption and activation behaviors over Fe<sub>3</sub>C catalysts. The distinctive micro-environment on the Fe<sub>3</sub>C surface made it more conducive to CO<sub>2</sub> adsorption and activation compared to other Fe-based catalysts, which could be further enhanced by the addition of multi-metal promotors. The electronic properties of promoters well explained their influence on CO<sub>2</sub> adsorption behavior, while the binding energy of promoters had a good linear relationship with the CO<sub>2</sub> activation barrier. Specifically, there existed a distance effect by the doped multi-metals. When the doped metals were adjacent to each other, it would be more beneficial for CO<sub>2</sub> dissociation, and when they were far away from each other, it facilitated CO<sub>2</sub> adsorption. Moreover, Mn atom is a good choice for forming dual-atom catalysts, which could significantly increase the adsorption stability of CO<sub>2</sub> and facilitate the direct dissociation of CO<sub>2</sub>. Catalysis ; Carbide ; Promoter ; Metal ; Materials science ; Nanotechnology ; Chemical engineering ; Chemistry ; Metallurgy ; Organic chemistry ; Engineering ; Gene ; Biochemistry Catalytic Processes in Materials Science ; Catalysts for Methane Reforming ; Catalysis and Oxidation Reactions
Authors: Shin Aizawa | Miyuki Yuda | Shuichi Hirai | Isao Tsuboi | Takashi Koike | Yoshihiro Hatta | Katsuhiro Miura | Masahiro Yasuda
Source: Preprints.org (preprint, 2025-10-14)
Field: Materials Science — Polymers and Plastics

Kinetics of Multiple Myeloma Derived Cloned MM1.S Cells in the Three-Dimensional Culture System Constructed by Polymer Particles and Bone Marrow Stromal Cells in the Presence of Proteasome Inhibitor, Bortezomib Background: The three-dimensional (3D) culture system that uses polymer particles with a bone marrow stroma cell feeder layer reproduces a biostructural hematopoiesis state effectively as compared to the conventional two-dimensional (2D) culture method. The 3D culture that maintains normal hematopoiesis, including prolongation of the hematopoietic stem cell proliferation and differentiation. The bone marrow stromal cells in a 3D culture, alter leukemic cell growth and protect the leukemic cells from anticancer agents. However, the mechanism of stromal cells on the hematopoietic stem cell proliferation and differentiation and neoplastic cells, including leukemia in the 3D culture, still bear many questions. Methods: We assessed the mechanism of two different bone marrow-derived stromal cells (i.e., MS-5 and Tst-4) bearing different characteristics, by using for a feeder layer in the 3D culture to compare the supportive action to leukemic cells. We focused on the role of the 3D culture constructed with the bone marrow stromal cells on the leukemic cell growth. Multiple myeloma cells are strongly related to the stromal cells in their proliferation; hence, the cloned MM1.S cells derived from multiple myeloma were cocultured in the 3D, and their cell growth was examined. We also examined the effect of the antineoplastic agent, bortezomib, which is a proteasome inhibitor, in the 3D culture system with a different stromal cell feeder. Results and conclusions: When MM1.S myeloma cells were cultured with MS-5 stroma in a 3D condition, the cell growth was found to be slow compared with that in the 2D culture and also with those in both the 2D and 3D cocultures with Tst-4 stroma. The MS-5 cells in the 3D culture protected the MM1.S cells from the cytocidal effect of the bortezomib treatment. Different kinetics of the MM1.S cells were observed depending on the stromal cells, suggesting their inherent and complicated characteristic. Stromal cell ; Bone marrow ; Cell culture ; Haematopoiesis ; Multiple myeloma ; Bortezomib ; Stem cell ; Proteasome inhibitor ; Cell growth Dendrimers and Hyperbranched Polymers ; Multiple Myeloma Research and Treatments
Authors: Mehdi Afshari-Bavil | Shiva Hayati Raad | Dong Liu
Source: Scientific Reports (article, 2025-11-30)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Multiband SERS substrate using switchable hot spots of the inline graphene-wrapped nanoparticle chains This paper discusses the applicability of graphene-based inline spherical trimers for the triple band single molecule detection of the analytes. The extension of the performance to the few particles' linear array assemblies with the aim of increasing the number of frequency bands and conducting hot-spot engineering is correspondingly provided. Numerical simulations show that the observed multi-band electric field intensities at the hot spots are adequately high to be used in single-molecule detection through surface-enhanced Raman scattering (SERS). Meanwhile, the few particles' linear array offers the hot spot switching capability regarding different frequencies. The generation of multiple resonances in the proposed devices is the consequence of strong coupling among the nanoparticles in the array. It is observed that to survive the higher-order resonance' detection capability, high-quality graphene shells are demanded, which is the main challenge of the experimental realization due to the imperfections introduced by the curvature of the particles. Also, to reach the single-molecule detection criteria, the use of hollow nanoparticles is a must. Importantly, multiple resonance generation employing multiple nanoparticles in the chain is not observed in the chains of plasmonic metallic particles. It is the outcome of electing graphene as the design platform since the plasmon lifetime and dissipation engineering are viable in the graphene-based devices. Nanoparticle ; Plasmon ; Raman scattering ; Substrate (aquarium) ; Electric field ; Plasmonic nanoparticles ; Graphene ; Hot spot (computer programming) ; Curvature Gold and Silver Nanoparticles Synthesis and Applications ; Plasmonic and Surface Plasmon Research ; Metamaterials and Metasurfaces Applications
Authors: Garrett LeCroy | Linu Malakkal | Michael E. Woods | Qiufeng Yang | Benjamin Beeler | Ruchi Gakhar
Source: ChemRxiv (preprint, 2025-04-25)
Field: Chemistry — Inorganic Chemistry

Versatile Cell Design for Molten Fluoride SaltSpectroscopy: Investigating Metal-IonSpeciation in High-Temperature eutecticLiF-NaF-KF Fluoride-based molten salts are candidate coolants and fuel salts in certain Generation IV molten salt reactors (MSRs). Effective monitoring of these salts is crucial, because salt composition plays a key role in reactor safety and efficiency. Optical probes offer a potentially powerful method of remotely monitoring fission and corrosion products within these salts, providing valuable data for reactor process control. However, performing spectroscopic measurements of fluoride-based salts is particularly challenging due to their highly corrosive nature, which can degrade many common optical materials. In this work, we present a novel optical cell design that enables spectroscopic measurements of transition-metal analytes in LiF-NaF-KF eutectic salt (i.e., FLiNaK). This innovative cell design overcomes the challenges posed by the corrosive nature of the salts, allowing for accurate and consistent spectroscopic analysis. This work reports temperature dependent absorption measurements for Co2+, Ni2+, and Cr3+ analytes, which are common corrosion products originating from structural alloys in MSR systems. Absorption spectra were used to understand interactions of these analytes with FLiNaK, particularly ligand field coordination. The analysis of absorption spectra was complemented by structural analyses using ab initio molecular dynamics (AIMD) simulations, providing deeper insights into the behavior of the analytes in FLiNaK. Our findings indicate that the analytes studied in this work exist in octahedral or near-octahedral coordination states that remain stable across the temperature range of 500-600°C. Eutectic system ; Fluoride ; Molten salt ; Materials science ; Metal ; Salt (chemistry) ; Spectroscopy ; Genetic algorithm ; Inorganic chemistry ; Metallurgy ; Chemistry ; Physical chemistry ; Alloy ; Physics Inorganic Fluorides and Related Compounds ; Molten salt chemistry and electrochemical processes
Authors: Houssem Boulebd
Source: RSC Advances (article, 2025-01-01)
Field: Chemistry — Organic Chemistry

Insights into the antioxidant activity and metal chelation capacity of natural marine bromophenols: role of C–O–C and C–C linkages and the catechol group Marine algae are an important source of phenolic compounds with multiple biological applications. Among them, bromophenols (BPs) show remarkable antioxidant activity <i>in vitro</i>, although their mechanisms of action remain poorly elucidated. In this study, we used density functional theory (DFT) calculations to explore in detail the antioxidant mechanism of two natural BPs (BP-I and BP-II), differing only in the bond linking their phenolic groups (C-O-C <i>vs.</i> C-C). The results revealed that both compounds are effective HOO˙ scavengers in lipid media, with respective rate constants of 2.40 × 10<sup>2</sup> and 1.76 × 10<sup>3</sup> M<sup>-1</sup> s<sup>-1</sup>, the BP-II derivative (C-C bond) proving more reactive than its BP-I counterpart (C-O-C bond). In aqueous media, their reactivity was comparable with high-rate constants of 1.96 × 10<sup>9</sup> and 2.04 × 10<sup>9</sup> M<sup>-1</sup> s<sup>-1</sup> but dependent on their protonation state. This high scavenging capacity is attributed to the deprotonated catechol group. In addition, both BPs showed a high chelation affinity for Cu(ii) ions, suggesting a secondary antioxidant activity (inhibition of free radical production through metal sequestration). This study sheds light on the antioxidant mechanisms of marine BPs and highlights the impact of the nature of the interphenolic bond (C-O-C or C-C) as well as the catechol group on their efficacy. Catechol ; Chemistry ; Chelation ; Antioxidant ; Potency ; Stereochemistry ; Metal ; Biochemistry ; Organic chemistry ; In vitro Free Radicals and Antioxidants ; Antioxidant Activity and Oxidative Stress ; Biochemical effects in animals
Authors: Sangita Sharma | Lalima Sharma | R. Rathore | D. Vijay | Mangal Shree Dulawat
Source: Asian Journal of Chemistry (article, 2025-05-27)
Field: Chemistry — Organic Chemistry

Synthesis, Structural Characterization and Anticancer Evaluation of 2-Aminobenzothiazole Derivative via Benzoyl Isothiocyanate 2-Aminobenzothiazole derivatives are well-established scaffolds in medicinal chemistry, valued for their diverse pharmacological profiles. In this study, a novel synthetic route led to the development of N-(1,3-benzothiazol-2-yl)benzamide (SIBO), whose structure was thoroughly characterized via FTIR, NMR, HRMS and SC-XRD techniques. The experimentally determined crystal geometry was further supported by DFT calculations at the B3LYP/6-31G(d,p) level, showing excellent agreement in bond parameters and a moderate HOMO–LUMO energy gap indicative of potential bioactivity. Hirshfeld surface analysis highlighted key intermolecular interactions contributing to the stability of the crystal lattice. Preliminary in vitro cytostatic screening against MDA-MB-231 and MCF-7 breast cancer cell lines revealed dose-dependent growth inhibition, with SIBO reducing MDA-MB-231 cell viability by up to 52% at 10 µg/mL. Although its efficacy was lower to that of standard adriamycin, the selective activity and structural simplicity of SIBO indicate its potential as a lead compound for the development of safer and tailored anticancer drugs. Chemistry ; Isothiocyanate ; Derivative (finance) ; Phenyl isothiocyanate ; Combinatorial chemistry ; Medicinal chemistry ; Organic chemistry Synthesis and biological activity ; Synthesis and Characterization of Heterocyclic Compounds ; Synthesis of Tetrazole Derivatives
Authors: P. Naveen | Gopi Mamidi
Source: Research Square (preprint, 2025-12-05)
Field: Chemistry — Inorganic Chemistry

Phytochemical Engineering of Vanadium Pentoxide Nanoparticles via Neem Extract: A Sustainable Platform for Dual Antidiabetic–Anticancer Therapy Nanoparticle ; Zeta potential ; Pentoxide ; HeLa ; Cytotoxicity ; Viability assay ; Reactive oxygen species ; Reducing agent Vanadium and Halogenation Chemistry ; Nanoparticles: synthesis and applications ; Transition Metal Oxide Nanomaterials
Authors: Jiaqi Chen | Zhiheng Deng | Haoxiang Li | Lei Liu
Source: Scientia Sinica Chimica (article, 2025-11-04)
Field: Chemistry — Organic Chemistry

Progress on molecular glue degraders 在靶向蛋白质降解治疗领域，分子胶降解剂（MGDs）凭借优异成药性，近年来广受关注。MGDs 可特异性招募 E3 泛素连接酶，进而调控泛素-蛋白酶体系统功能。本文围绕两方面综述MGDs 的发现历程与作用机制研究：其一，系统总结 MGDs 辅助 E3 泛素连接酶介导底物蛋白泛素化的作用机制，详细阐述其通过诱导蛋白质构象改变、重塑分子间相互作用界面，进而高效促成 E3 泛素连接酶与靶蛋白的特异性结合，最终触发后续泛素化级联反应的完整过程；其二，系统探讨新型 MGDs 的开发策略及新底物蛋白的发现方法，涵盖基于分子文库的高通量筛选、化学蛋白质组学等技术的创新应用，以及数据驱动的底物预测模型构建等方向。 GLUE ; Component (thermodynamics) ; Yield (engineering) ; Work (physics) Click Chemistry and Applications ; Protein Degradation and Inhibitors ; Hydrogels: synthesis, properties, applications
Authors: Prisca Caesa Moneteringtyas
Source: JURNAL REDOKS ( JURNAL PENDIDIKAN KIMIA DAN ILMU KIMIA ) (article, 2025-07-31)
Field: Chemistry — Spectroscopy

Optimasi Geometri Senyawa Hidroksiklorokuin (HCQ) Menggunakan Pendekatan DFT dengan Basis 6-311G Penelitian ini bertujuan untuk menentukan metode kimia komputasi yang paling sesuai dalam mengoptimasi geometri senyawa hidroksiklorokuin (HCQ) sebagai turunan dari klorokuin (CQ). Tiga pendekatan kalkulasi kuantum digunakan dalam studi ini, yaitu metode semi-empiris (PM3, AM1, PM6), Hartree-Fock (HF), dan Density Functional Theory (DFT) dengan variasi himpunan basis (3-21G, 6-31G, dan 6-311G). Evaluasi dilakukan melalui perbandingan nilai pergeseran kimia (δ, ppm) ¹H-NMR hasil perhitungan terhadap data eksperimen. Parameter statistik yang digunakan meliputi nilai PRESS (Predicted Residual Error Sum of Squares) dan koefisien determinasi (r²). Hasil menunjukkan bahwa metode DFT dengan himpunan basis 6-311G menghasilkan nilai PRESS terendah (5,0892) dan r² paling mendekati 1 (0,9695), menandakan kesesuaian tertinggi dengan data eksperimen. Optimasi geometri juga menunjukkan bahwa struktur HCQ mengalami perubahan konformasi menuju bentuk paling stabil. Oleh karena itu, metode DFT 6-311G direkomendasikan sebagai pendekatan yang andal dan representatif dalam pemodelan struktur molekul HCQ secara teoretis. Chemistry Molecular spectroscopy and chirality
Authors: Taiwo Abayomi Banjo | Michael Olubusayo Binuyo | Willie Siyanbola | J. S. Ashidi | Ngozi Mirabel Otuonye | Wasiu Bamidele Mutiu | Saheed Adekunle Akinola | RA Akindele | Rasheed Omotayo Adeyemo | Oluwabunmi Fatungase | Hubert Kageruka | Chinedum Taahie Oparaugo | Farouk Adedeji Oladoja | A. A. Adedeji | Ebelechukwu Eugenia Afocha | Latif Kazim
Source: Rwanda Journal of Medicine and Health Sciences (article, 2025-07-31)
Field: Chemistry — Physical and Theoretical Chemistry

Tumor Necrosis Factor-Alpha (TNF- α) and Antiviral Activities of Artemisia SPP. Extracts on SARS-COV2 Artemisia spp. promises antiviral-proinflammatory cytokine regulation, justifying clinical COVID-19 prophylaxis/therapeutic research, especially against resistant SARS-CoV-2 variants. This could reduce vaccination dependency in impoverished nations while addressing vaccine efficacy and local immunity gaps. Tumor necrosis factor alpha ; Necrosis ; Virology ; Microbiology ; Immunology ; Biology ; Medicine ; Pathology thermodynamics and calorimetric analyses
Authors: Thị Nga Nguyễn | Đức Thiện Nguyễn | Thị Minh Huyền Võ | Thị Phương Thảo Nguyễn | Tiến Anh Dương
Source: Tạp chí Nghiên cứu Khoa học và Phát triển (article, 2025-09-30)
Field: Chemistry — Organic Chemistry

TỔNG QUAN VỀ NGUỒN GỐC TỰ NHIÊN VÀ PHƯƠNG PHÁP TỔNG HỢP INDIRUBIN Indirubin là thành phần hoạt chất quan trọng có trong 2 bài thuốc y học cổ truyền Trung Hoa là Danggui Longhui Wan và Qingdai. Từ những năm 1980, indirubin đã được sử dụng trên lâm sàng trong điều trị bệnh bạch cầu mạn dòng tủy. Tuy nhiên, do hạn chế về dược động học và hiệu quả điều trị, hàng loạt dẫn chất của indirubin đã được thiết kế và tổng hợp nhằm cải thiện những nhược điểm trên. Nghiên cứu tổng quan này được thực hiện nhằm mục đích hệ thống hóa về nguồn gốc tự nhiên cũng như phương pháp tổng hợp indirubin và các dẫn chất. Về nguồn gốc tự nhiên, các hợp chất indirubin có thể được chiết xuất từ thực vật, động vật thân mềm và một số chủng vi khuẩn tái tổ hợp. Bên cạnh đó, các indirubin cũng có thể thu được bằng con đường sinh học hoặc tổng hợp hóa học, đi từ nguyên liệu đầu là dẫn xuất của isatin và indol. Trong đó, phương pháp sinh tổng hợp sử dụng enzym đặc hiệu có nhiều tiềm năng ứng dụng trong sản xuất các indirubin ở quy mô công nghiệp trong tương lai gần. Indirubin ; Fumarase ; Tibetan medicine ; Christian ministry Synthesis and Biological Evaluation ; Pesticide and Herbicide Environmental Studies
Authors: Ye Zheng | Zhenyu Chen | Guy J. Clarkson | Stephen Marshall | Jianliang Xiao | Christopher J. Schofield | Martin Wills | Andrew V. Stachulski
Source: Royal Society Open Science (article, 2025-02-01)
Field: Chemistry — Inorganic Chemistry

Dynamic kinetic resolution-mediated synthesis of C-3 hydroxylated arginine derivatives Hydroxylated amino acids and their derivatives, including those found in proteins, are important in biology and medicinal chemistry. Incubation of N-acetyl-l-arginine with clavaminic acid synthase, a key oxygenase in clavulanic acid biosynthesis, affords a (3R)-hydroxylated product that is identical to material obtained by total synthesis from Boc-beta alanine. The key step employed dynamic kinetic resolution (DKR) of a β-ketoester precursor, achieved in high diastereomeric and enantiomeric excess using an (R)-SEGPHOS/Ru(II) catalyst. The results highlight the utility of DKR for the preparation of C-3 hydroxylated amino acid derivatives. Kinetic resolution ; Enantiomer ; Chemistry ; Diastereomer ; Amino acid ; Enantioselective synthesis ; Arginine ; Biosynthesis ; Stereochemistry ; Catalysis ; Alanine ; Biocatalysis ; Enzyme ; Organic chemistry ; Biochemistry ; Reaction mechanism Asymmetric Hydrogenation and Catalysis ; Synthetic Organic Chemistry Methods ; Chemical Synthesis and Analysis