jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Wentao Huang | Jakob K. Reinhardt | Aiping Tian | Xiao Zhang | Binghui Li | Noah Gould | Sashirekha Nallapati | Kimberley L. Alexander | Yi Wang | Jason J. Guo | David E. Budil | Jing‐Ke Weng
Source: Angewandte Chemie International Edition (article, 2025-08-22)
Field: Chemistry — Inorganic Chemistry

Cyclochlorotine Hydroxylase CctR Reveals DUF3328 as a Family of Copper‐Dependent Metalloenzymes DUF3328 is a protein family widely found in fungal natural product biosynthesis pathways. Although DUF3328 proteins have long been implicated in diverse modifications of inert C(sp<sup>3</sup>)─H bonds, including halogenation, hydroxylation, and macrocyclization, the biochemical properties and catalytic mechanisms of DUF3328 proteins remain elusive. Here, we report the characterization of the DUF3328 protein CctR, which catalyzes C(sp<sup>3</sup>)─H hydroxylation of fungal cyclic peptide cyclochlorotine. Through AlphaFold modeling, in vitro biochemical characterization, and spectroscopic analysis, we demonstrate that CctR is a membrane-associated copper-dependent enzyme that functions as a homodimer. The dimerization of CctR is mediated by its transmembrane helix, a four-helix coiled coil, and C-terminal disulfide bonds. The conserved HxxHC(x)<sub>n</sub>HxxHC motif, characteristic of the DUF3328 superfamily, is anchored on the dimerization interface and forms a binuclear copper coordination center. Moreover, we show that CctR is dioxygen-dependent and requires electron input for the hydroxylation reaction. Together, these findings define DUF3328 as a previously unrecognized family of binuclear copper-dependent metalloenzymes, capable of catalyzing diverse chemical transformations, and lay the groundwork for future discovery of novel biocatalysts within this widespread enzyme class. Copper ; Chemistry ; Organic chemistry Metal-Catalyzed Oxygenation Mechanisms ; Porphyrin Metabolism and Disorders ; Enzyme Structure and Function
Authors: Wentao Huang | Jakob K. Reinhardt | Aiping Tian | Xiao Zhang | Binghui Li | Noah Gould | Sashirekha Nallapati | Kimberley L. Alexander | Yi Wang | Jason J. Guo | David E. Budil | Jing‐Ke Weng
Source: Angewandte Chemie (article, 2025-08-22)
Field: Chemistry — Inorganic Chemistry

Cyclochlorotine Hydroxylase CctR Reveals DUF3328 as a Family of Copper‐Dependent Metalloenzymes Abstract DUF3328 is a protein family widely found in fungal natural product biosynthesis pathways. Although DUF3328 proteins have long been implicated in diverse modifications of inert C( sp 3 )─H bonds, including halogenation, hydroxylation, and macrocyclization, the biochemical properties and catalytic mechanisms of DUF3328 proteins remain elusive. Here, we report the characterization of the DUF3328 protein CctR, which catalyzes C( sp 3 )─H hydroxylation of fungal cyclic peptide cyclochlorotine. Through AlphaFold modeling, in vitro biochemical characterization, and spectroscopic analysis, we demonstrate that CctR is a membrane‐associated copper‐dependent enzyme that functions as a homodimer. The dimerization of CctR is mediated by its transmembrane helix, a four‐helix coiled coil, and C‐terminal disulfide bonds. The conserved HxxHC(x) n HxxHC motif, characteristic of the DUF3328 superfamily, is anchored on the dimerization interface and forms a binuclear copper coordination center. Moreover, we show that CctR is dioxygen‐dependent and requires electron input for the hydroxylation reaction. Together, these findings define DUF3328 as a previously unrecognized family of binuclear copper‐dependent metalloenzymes, capable of catalyzing diverse chemical transformations, and lay the groundwork for future discovery of novel biocatalysts within this widespread enzyme class. Copper ; Chemistry ; Organic chemistry Metal-Catalyzed Oxygenation Mechanisms ; Porphyrin Metabolism and Disorders ; Enzyme Structure and Function
Authors: Weixuan Zhao | Nianyin Li | Jianhua Zhao | Yao Yao | Feng Jiang | Yuan Wang | Zhifei Sun | Jiaqing You | Changan Du | Xiao-jun Cai | Hao Lei | Fei Tian | Long Chen
Source: Journal of Petroleum Exploration and Production Technology (article, 2025-09-27)
Field: Materials Science — Materials Chemistry

Preparation and performance evaluation of ultra high temperature corrosion inhibitor for acidizing Abstract To develop efficient acid corrosion inhibitors suitable for oilfield environments, this study integrates quantum chemical calculations and molecular dynamics simulations to assess four Mannich base compounds. The molecular structures were analyzed in terms of electronic properties and adsorption behavior on Fe surfaces. All four molecules exhibited multiple reactive centers—including carbonyl groups, C = C bonds, amino groups, and aromatic rings—facilitating electron exchange and protective film formation via chemisorption. Among them, compound X4 exhibited the highest adsorption energy and the lowest diffusion coefficient for corrosive species (H₂O/H₃O⁺), indicating superior theoretical corrosion inhibition performance. Based on these findings, X4 was synthesized through a two-step Mannich reaction. The optimal synthesis conditions were determined using single-factor experiments and orthogonal design optimization. The synthesized product was characterized using FTIR(Fourier Transform Infrared Spectroscopy). The corrosion inhibition performance was evaluated by weight-loss measurements under varying temperatures, acid concentrations, and metal substrates. X4 exhibited excellent corrosion inhibition for N80, 13Cr, and P110 steels, maintaining its effectiveness at temperatures up to 180 °C. The adsorption of X4 followed the Langmuir isotherm model and was predominantly governed by chemisorption, aligning well with simulation predictions. This integrated computational–experimental approach offers a robust framework for the rational design of high-performance corrosion inhibitors suitable for harsh acidic environments in the petroleum industry. Corrosion ; Adsorption ; Corrosion inhibitor ; Langmuir adsorption model ; Diffusion ; Molecular dynamics ; Metal ; Molecule Corrosion Behavior and Inhibition ; Hydrogen embrittlement and corrosion behaviors in metals ; Concrete Corrosion and Durability
Authors: Vikas Kumar Jha | Sunil Kumar Patel | Devarapalli Chenna Rao | Kovuru Gopalaiah | E. Siva Subramaniam Iyer
Source: RSC Advances (article, 2025-01-01)
Field: Chemistry — Organic Chemistry

The enhanced ultrafast dissociation of <i>meso</i>-hydrogen of bis(indolyl)methane derivatives under acidic conditions Bis(indolyl)methane (BIM) derivatives are an important class of molecules that have shown vivid applications. The photo dynamics of BIM derivatives has been studied through ultrafast spectroscopy. It has been observed that the acidic medium plays a vital role in governing the spectral characteristics of BIMs, imputing to the ambivalent nature of BIMs under acidic conditions. We noticed that the dissociation of <i>meso</i>-hydrogen is enhanced under acidic conditions, while no such enhancement is observed under alkaline and neutral conditions. We further perceived that the dissociation of <i>meso</i>-hydrogen takes precedence over the dissociation of N-H bonds, even in an acidic medium. Quantum chemical calculations support the experimental observations. Although the functionalisation with electron-withdrawing or electron-donating groups seems to affect photophysical properties such as spectral shift, quantum yield, <i>etc.</i>, tuning the acidic medium plays a significant role. Dissociation (chemistry) ; Methane ; Chemistry ; Ultrashort pulse ; Photochemistry ; Molecule ; Hydrogen ; Physical chemistry ; Organic chemistry ; Laser ; Physics ; Optics Synthesis of Indole Derivatives ; Molecular Sensors and Ion Detection ; Photochromic and Fluorescence Chemistry
Authors: Geetanjali Deka | Arisha Arora | Priyanka Bhat | Vandna Singh | Hari Mohan | S Senthil Kumaran | Chandan Mukherjee
Source: Small (article, 2025-08-13)
Field: Materials Science — Materials Chemistry

Liver‐Directing Fe(III)‐Based MRI Contrast Agent Liver cancer has been identified as the second most common cause of cancer-related mortality. Routine liver diagnosis by recording magnetic resonance (MR) images in the presence of a liver-directing contrast agent (CA) can recognize any abnormalities early. However, the clinically approved liver-specific Gd(III)-based CAs are of great concern for bio-safety. In fact, several medical agencies have restricted the usage of such CAs. Thus, to develop non-Gd-based biocompatible CAs for liver imaging, a thermodynamically stable and kinetically inert nonaquated six-coordinate paramagnetic Fe(III)-complex (1) is confined within a biocompatible porous silica nanoparticle of size about 18 nm. Such entrapment has boosted the longitudinal relaxivity value of Complex 1 (r<sub>1</sub> = 0.59 × 10<sup>-3</sup> m<sup>-1</sup>s<sup>-1</sup>) upto 9 times to 5.36 × 10<sup>-3</sup> m<sup>-1</sup>s<sup>-1</sup>, which further increased to 10.83 × 10<sup>-3</sup> m<sup>-1</sup>s<sup>-1</sup> in the presence of 0.67 × 10<sup>-3</sup> m concentration of serum albumin protein. Surface functionalization of the nanoparticle with hydrophobic p-methoxybenzamide (C1@SiO<sub>2</sub>-PMBA-NP) facilitates HepG2 cell internalization as evinced by in vitro fluorescent images and flow cytometry analyses. Time-dependent contrast changes in the liver MR images recorded on C57BL/6 mice in a preclinical MRI instrument establish the applicability of the biocompatible C1@SiO<sub>2</sub>-PMBA-NP as the T<sub>1</sub>-weighted liver-directing CA for magnetic resonance imaging (MRI). Contrast (vision) ; MRI contrast agent ; Materials science ; Nuclear magnetic resonance ; Nanotechnology ; Computer science ; Artificial intelligence ; Nanoparticle ; Physics Lanthanide and Transition Metal Complexes ; MRI in cancer diagnosis ; Advanced MRI Techniques and Applications
Authors: Yohei Adachi | Maho Kurihara | Shota Hosoya | Shota Terao | Masashi Nakamura | Yuichi Kitagawa | Yasuchika Hasegawa | Joji Ohshita
Source: Advanced Optical Materials (article, 2025-06-26)
Field: Materials Science — Materials Chemistry

Drastic Mechanochromic Luminescence Through Fluorescence–Phosphorescence Switching in a Heavy‐Atom‐Free Organoboron Compound Abstract Fluorescence and phosphorescence are emissions from molecules in the lowest excited singlet state (S 1 ) and the lowest triplet state (T 1 ), respectively. Generally, as the S 1 and T 1 energy levels are different, the fluorescence and phosphorescence wavelengths are also different. By switching between these emissions through mechanical stimuli, a drastic change in emission color can be achieved. However, organic molecules typically have low intersystem crossing efficiency, making it difficult for them to exhibit phosphorescence. Therefore, organic dyes that exhibit remarkable mechanochromic luminescence (MCL) via the switching between thermally activated delayed fluorescence (TADF) and room‐temperature phosphorescence (RTP) are extremely limited. In this study, heavy‐atom‐free molecules are synthesized. One of them, which has a bulky amino group to a benzodithienoborepin core, exhibited green TADF in solution and the amorphous state, and orange RTP in the crystalline state. This switching between TADF and RTP is enabled by mechanical grinding. Furthermore, DFT calculations and single‐crystal X‐ray structural analysis revealed that the twisting of the bulky amino group in the crystalline state induces the switching between TADF and RTP. Phosphorescence ; Materials science ; Luminescence ; Fluorescence ; Persistent luminescence ; Photochemistry ; Atom (system on chip) ; Optoelectronics ; Optics ; Thermoluminescence ; Chemistry ; Physics Luminescence and Fluorescent Materials ; Molecular Sensors and Ion Detection ; Organoboron and organosilicon chemistry
Authors: Fernando Lehue | Carlos Coronel‐Oliveros | Vicente Medel | Thomas Liebe | Jörn Kaufmann | Sebastián Orellana | Diego Becerra | Enzo Tagliazucchi | Patricio Orio
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2025-02-06)
Field: Chemistry — Electrochemistry

Noradrenaline and Acetylcholine shape Functional Connectivity organization of NREM substages: an empirical and simulation study Abstract Sleep onset is characterized by a departure from arousal, and can be separated into well-differentiated stages: NREM (which encompasses three substages: N1, N2 and N3) and REM (Rapid Eye Movement). Awake brain dynamics are maintained by various wake-promoting mechanisms, particularly the neuromodulators Acetylcholine (ACh) and Noradrenaline (NA), whose levels naturally decrease during the transition to sleep. The combined influence of these neurotransmitters on brain connectivity during sleep remains unclear, as previous models have examined them mostly in isolation or only in deep sleep. In this study, we employ a Whole Brain model to investigate how changes in brain neurochemistry during NREM sleep, specifically involving ACh and NA, affect the Functional Connectivity (FC) of the brain. Using a Wilson-Cowan whole brain model informed by an empirical connectome and a heterogeneous receptivity map of neuromodulators, we explore these dynamics. Initial FC analysis reveals distinct connectivity changes: a decrease in Locus Coeruleus (LC) connectivity with the cortex during N2 and N3, and a decrease in Basal Forebrain (BF) connectivity with the cortex during N3. Additionally, compared to Wakefulness (W), there is a transition to a more integrated state in N1 and a more segregated state in N3. We adjust the coupling and input-output slope of the Whole Brain model for ACh and NA, based on BF or LC priors, to show that region-specific neurotransmitter distribution is key to explaining their effects on FC. This work enhances our understanding of neurotransmitters’ roles in modulating sleep stages and their significant contribution to brain state transitions between different states of consciousness, both in health and disease. Acetylcholine ; Non-rapid eye movement sleep ; Neuroscience ; Psychology ; Internal medicine ; Medicine ; Electroencephalography Electrochemical Analysis and Applications ; Neuroscience and Neuropharmacology Research ; Computational Drug Discovery Methods
Authors: Naohiko Yoshikai | Shunya Morohashi | Liejin Zhou | Kazuya Kanemoto | Eunsang Kwon
Source: ChemRxiv (preprint, 2025-02-20)
Field: Chemistry — Organic Chemistry

Hexadehydro Diels–Alder/Alkynyliodanation Cascade: A Highly Regioselective and Expedient Entry to Polycyclic Aromatics We report here a cascade process that integrates the hexadehydro Diels–Alder (HDDA) reaction with alkynyliodanation of the resulting aryne, enabling the efficient synthesis of highly substituted aryl-λ3-iodanes. By simply heating a mixture of a tetrayne, consisting of tethered 1,3-diynes, and an alkynylbenziodoxole, the tetrayne-derived aryne undergoes highly regioselective insertion into the alkynyl–iodine(III) bond, producing a 1,4-dialkynyl-2-iodanyl-3-arylbenzene derivative in good yield. Notably, the observed regioselectivity contrasts with the typical regioselectivity patterns reported in related HDDA/aryne trapping reactions, likely due to steric factors influencing the four-centered transition states. The unique regiochemical arrangement of the iodanyl, alkynyl, and aryl substituents offers a versatile platform for subsequent π-extension reactions. These downstream transformations enable the divergent construction of polyaromatic frameworks, such as helicenes and cyclopenta[cd]pyrenes, underscoring the utility of aryne carboiodanation in complex aromatic synthesis. Regioselectivity ; Cascade ; Alder ; Chemistry ; Diels–Alder reaction ; Organic chemistry ; Biology ; Botany ; Chromatography ; Catalysis Asymmetric Synthesis and Catalysis ; Chemical Synthesis and Analysis ; Coordination Chemistry and Organometallics
Authors: Fan Shao | Renting Jiang | Linhu Li | Yaxuan Lu | Mingyang Chen | Jinghang Li | Bang Liu | Ming Li
Source: Advanced Functional Materials (article, 2025-06-25)
Field: Materials Science — Materials Chemistry

Near‐Infrared‐II Plasmonic Multi‐Enzyme Nanocapsules for Hyperthermia‐Augmented Cascade Catalytic Oncotherapy Abstract Catalytic therapy based on artificial nanozymes holds considerable potential for cancer treatment but faces clinical challenges due to insufficient catalytic activity, limited enzymatic diversity, and the adaptive antioxidant tumor microenvironment. Herein, a near‐infrared II (NIR‐II) plasmonic multi‐enzyme capsule (PdCu‐pNS capsule) is developed to augment cascade catalytic therapy through hyperthermia synergy. The capsule structure integrates a NIR‐II plasmonic porous AuAg nanoshell (pNS) core with PdCu nanozymes, co‐encapsulated within a PEGylated silica nanocapsule. The PdCu‐pNS capsules exhibit distinct multi‐enzymatic activities, including peroxidase, catalase (CAT)‐, oxidase (OXD)‐, and glutathione peroxidase (GPx)‐like activities. Mechanistically, the CAT‐like activity sustains intratumoral O 2 supply to alleviate hypoxia while synergistically promoting • O 2 ˉ generation with the OXD‐like catalysis. Concurrently, the GPx‐mimetic activity depletes intracellular glutathione, thereby disrupting redox homeostasis in cancer cells. Notably, the NIR‐II plasmonic heating effects enhance enzymatic activities while enabling spatiotemporally controlled hyperthermia‐mediated tumor ablation. In vivo evaluations demonstrate exceptional therapeutic efficacy with an 87.7% tumor growth inhibition rate in 4T1 tumor‐bearing mice via the combinational catalytic‐hyperthermia therapy following intravenous administration of PdCu‐pNS capsules, Collectively, this work presents a multifunctional platform that synergizes multi‐enzyme cascades with plasmon resonance for improved therapeutic outcomes of catalytic therapy. Materials science ; Nanocapsules ; Plasmon ; Cascade ; Catalysis ; Hyperthermia ; Infrared ; Nanotechnology ; Nanoparticle ; Optoelectronics ; Chemical engineering ; Optics ; Organic chemistry ; Medicine ; Chemistry Advanced Nanomaterials in Catalysis ; Nanoplatforms for cancer theranostics ; Carbon and Quantum Dots Applications
Authors: Soo‐Jin Kim | Mi‐Sun Choi | Hyun Jegal | Min Beom Heo | Minjeong Kwak | Hyun Kyong Shon | Seungwoo Song | Tae Geol Lee | Ji Ho Park | Dong Woo Lee | Seokjoo Yoon | Jung‐Hwa Oh
Source: Journal of Biological Engineering (article, 2025-07-01)
Field: Materials Science — Materials Chemistry

New approach methodologies for in vitro toxicity screening of nanomaterial using a pulmonary three-dimensional floating extracellular matrix model By reducing the uncertainties associated with the sedimentation and optical interference of nanomaterials, our 3D model provided a more precise analysis of cytotoxicity. This study highlights the potential of using new approach methodologies and improved HTS approaches to enhance the efficiency and accuracy of risk assessment protocols for emerging nanomaterials. Extracellular matrix ; In vitro ; Matrix (chemical analysis) ; Nanomaterials ; Pulmonary toxicity ; Computer science ; Cell biology ; Toxicity ; Chemistry ; Nanotechnology ; Medicine ; Materials science ; Biology ; Biochemistry ; Internal medicine Nanoparticles: synthesis and applications ; Graphene and Nanomaterials Applications ; 3D Printing in Biomedical Research
Authors: Xiaojun Wei | Xin Luo | Futian Wang | Junxiong Huang | Feibing Xiong | Weiya Zhou | Huaping Liu
Source: Advanced Materials Interfaces (article, 2025-09-01)
Field: Materials Science — Materials Chemistry

Manipulating the Chiral Self‐Assembly of Achiral Porphyrin Molecules with Carbon Nanotubes as Templates Abstract The chiral self‐assembly of achiral molecules has sparked significant interest because of its capacity to transcend the intrinsic properties of achiral monomers while eliciting emergent chiral characteristics and applications. Herein, the study presents a systematic investigation of achiral tetraphenyl porphyrin (TPP) self‐assembly utilizing chirality‐sorted achiral (10,0) single‐wall carbon nanotubes (SWCNTs) as structuring templates. Comprehensive characterization through optical absorption and photoluminescence spectroscopies confirms the effective stacking of non‐water‐soluble TPP molecules onto nanotube surfaces within surfactant‐stabilized aqueous media, achieved through optimized ultrasonication and centrifugation processes. Notably, a robust bisignate circular dichroism signal is detected for the stacked TPPs, providing definitive spectroscopic evidence of the chiral self‐assembly of inherently achiral TPP molecules into optically active helical architectures on SWCNT templates. Furthermore, the current chiral self‐assembly of TPP molecules driven by strong π–stacking interactions with SWCNTs is further verified to exhibit reversible thermodynamic behaviour, which can be precisely manipulated through the TPP/SWCNT concentration ratio and environmental temperature. The findings establish a versatile platform consisting of 1D SWCNT templates for inducing and manipulating chirality in achiral molecular systems and provide fundamental insights critical for advancing chiral recognition/sensing technologies and enantioselective catalysis applications. Materials science ; Porphyrin ; Template ; Carbon nanotube ; Nanotechnology ; Molecule ; Self-assembly ; Chirality (physics) ; Carbon nanobud ; Organic chemistry ; Nanotube ; Optical properties of carbon nanotubes ; Chiral symmetry Porphyrin and Phthalocyanine Chemistry ; Surface Chemistry and Catalysis ; Supramolecular Self-Assembly in Materials
Authors: Jian Lu | Jiang-Feng Wu | Jian‐Liang Ye | Pei‐Qiang Huang
Source: Beilstein Journal of Organic Chemistry (article, 2025-10-13)
Field: Chemistry — Organic Chemistry

Further elaboration of the stereodivergent approach to chaetominine-type alkaloids: synthesis of the reported structures of aspera chaetominines A and B and revised structure of aspera chaetominine B We report herein the fourth generation of our synthetic strategy to chaetominine-type alkaloids featuring two modifications of the last step of our 4 to 6-step approach. Firstly, by employing EDCI/HOBt as the coupling system for the last step of the one-pot <i>O</i>-debenzylation-lactamization reaction, the overall yield of our previous total synthesis of (-)-isochaetominine A was increased from 25.4% to 30.8% over five steps. Secondly, a new protocol featuring the use of an aged solution of K<sub>2</sub>CO<sub>3</sub>/MeOH to quench the DMDO epoxidation-triggered cascade reaction was developed, which allowed the in situ selective mono- or double epimerization at C11/C14 as shown by the diastereodivergent synthesis of a pair of diastereomers of versiquinazoline H from its tripeptide precursor. This double epimerization at the last-step allowed the enantiodivergent synthesis of two enantiomers in either racemate form or two pure enantiomers from the same precursor. The former was demonstrated by the synthesis of alkaloid 14-<i>epi</i>-isochaetominine C that was used to determine the enantiomeric excess of the synthesized natural product (98.7% ee), while the latter was illustrated by the synthesis of both enantiomers of the alkaloid isochaetominine. Additionally, the reported structures of alkaloids aspera chaetominines A and B have been synthesized. Moreover, the four-step synthesis of the reported structure of aspera chaetominine B generated another diastereomer that was converted in one-pot to (-)-isochaetominine C, which turned out to be the revised structure of aspera chaetominine B. Diastereomer ; Epimer ; Total synthesis ; Enantiomer ; Natural product ; Tripeptide ; Alkaloid ; Yield (engineering) Advanced Synthetic Organic Chemistry ; Alkaloids: synthesis and pharmacology ; Chemical Synthesis and Analysis