We present TUNA, an open-source quantum chemistry program specifically designed for atoms and diatomic molecules. Within this narrow molecular domain, a broad and consistent set of electronic structure methods and calculation types is available. Energies, optimisations, vibrational frequencies, response properties, coordinate scans and ab initio molecular dynamics trajectories can be accessed through an intuitive command-line interface. A single principle underlies TUNA: once a method can be used to evaluate the energy, all properties follow from numerical differentiation. This makes the program both a transparent teaching platform and a compact environment for benchmarking methods on diatomics $\unicode{x2014}$ among the most simple yet instructive systems in quantum chemistry. Reference implementations including density functional theory, many-body perturbation theory and coupled cluster theory, supported by detailed theoretical documentation, make TUNA an accessible foundation for developing improved methods and algorithms in electronic structure.
Nonequilibrium chemistry is central to many astrophysical environments but remains a major computational bottleneck in simulations because solving the associated stiff ODE systems is expensive. Neural surrogates promise large speedups, yet existing studies rarely provide systematic comparisons of architectures or rigorous optimization toward both accuracy and efficiency. We introduce CODES, a principled framework for optimizing and benchmarking astrochemical surrogate models. Using CODES, we compare four neural surrogate architectures across four KROME-generated datasets spanning primordial and molecular-cloud chemistry with up to 287 reactions across 37 species. Dual-objective optimization reveals pronounced accuracy-efficiency trade-offs across architectures. Fully connected models achieve the highest accuracy and most reliable uncertainty estimates, while latent-evolution models show improved robustness under iterative prediction. Our results highlight the importance of systematic optimization and architectural comparison. The datasets, metrics, and benchmarking procedure are publicly released within CODES to enable reproducible surrogate benchmarking.
Do Hoang Giang, Bui Thi Nhat Le, Nguyen Thi Thu Minh
et al.
This study investigates the optimal conditions to enrich the phenolic content of the extract from Pandanus amaryllifolius leaves and evaluates the bioactivities of this enrichment. The phenolic enrichment was prepared under optimized conditions using the response surface methodology (RSM) with the Box–Behnken design. The antioxidant properties were assessed using DPPH and hydroxyl radical scavenging assays, while the NO production inhibition was measured in LPS-stimulated RAW 264.7 macrophage cells. Results indicated that the phenolic enrichment showed potent antioxidant activity comparable to ascorbic acid and catechin and significantly higher NO inhibition than the separated nonalkaloid and alkaloid fractions. The study also highlights the synergistic effect of phenolic and alkaloid compounds on the antioxidants and anti-inflammatory activities of the phenolic enrichment from Pandanus amaryllifolius leaves.
Bouchra Rossafi, Amal Bouribab, Oussama Abchir
et al.
The fight against diabetes mellitus remains a major global challenge due to its increasing prevalence, severe health complications, and the need to develop new therapeutic alternatives that are both effective and accessible to improve patient care. The current medications used to combat this disease have limitations, including side effects, which highlight the need for innovative and safer therapeutic approaches capable of specifically targeting key enzymes involved in carbohydrate metabolism, such as alpha-amylase and alpha-glucosidase. In this study, we explored the inhibitory potential of 386 phytochemical compounds extracted from Moroccan plants using an in-silico approach combining virtual screening via molecular docking, ADMET predictions, molecular dynamics simulations and MM/GBSA calculations. Among these evaluated compounds, two promising molecules were identified: myricetin (compound 276) and cholesterol (compound 290), both derived from the same plant, Ajuga iva L. These molecules exhibited strong binding affinities to the enzymes alpha-amylase and alpha-glucosidase, remarkable stability during MD simulations, and a favorable pharmacokinetic profile. These findings highlight the potential of Moroccan phytochemical compounds as natural inhibitors, paving the way for future experimental studies to develop them into antidiabetic treatments.
Characterizing temperate exoplanet atmospheres remains challenging due to their small size and low temperatures. Recent JWST observations provide valuable data, but their interpretation has led to diverging conclusions. Complementary approaches combining laboratory experiments and photochemical modeling are essential for constraining atmospheric chemistry and interpreting observations. We aim to identify chemical pathways governing the formation and evolution of neutral species and to assess their sensitivity to key parameters such as C/O ratio and metallicity. Our approach combines experimental and numerical simulations on H2-rich gas mixtures representative of sub-Neptune atmospheres, spanning a wide range of CH4, CO, and CO2 mixing ratios. A cold plasma reactor simulates out-of-equilibrium upper-atmospheric chemistry. A 0D photochemical model reproduces reactor conditions, guiding interpretation of key pathways and abundance trends. We observe the formation of both reduced and oxidized organic compounds. In CH4-rich mixtures, hydrocarbons form efficiently through methane chemistry, correlating with CH4 concentration and agreeing with models. In more oxidizing environments, particularly CO2-rich mixtures, hydrocarbon formation is inhibited by complex reaction networks and oxidative losses. Oxygen incorporation enhances chemical diversity and promotes formation of oxidized organic compounds of prebiotic interest (H2CO, CH3OH, CH3CHO), especially in atmospheres containing both CH4 and CO2. Atmospheres containing CH4 and CO, which balance carbon and oxygen supply without excessive oxidative destruction, favor efficient production of hydrocarbons and oxidized compounds. Out-of-equilibrium chemistry plays a key role in the diversification and organic complexification of temperate exoplanet atmospheres.
Manoj Kumar Deka, Akramul Ansary, Tridib Kumar Das
et al.
This study evaluates three spectrophotometric techniques for quantifying a binary combination of raloxifene and aspirin in terms of whiteness and greenness. Application of green and white analytical chemistry has gained widespread acceptance in the analytical community. The whiteness and greenness of the assessment were evaluated using three approaches: Complex green analytical procedure index, Analytical GREEnness calculator and Red Green Blue additive model. The technique (I) uses the simultaneous equation methodology for raloxifene at 285 nm and aspirin at 222 nm, respectively. Method (II) includes the area under the curve operating at (280–290) nm and (217–227) nm for raloxifene and aspirin, respectively. Method (III) operates using the first derivative method for raloxifene at 269 nm and aspirin at 216 nm. The linearity range was 2–14 µg/ml for three methods. P-Values were found satisfactory at a 95 % level of confidence. These techniques were intended for the binary mixture analysis in investigational formulations with high recoveries. The developed methods were validated according to ICH guidelines. These developed methods have been utilized in routine analysis to simultaneously determine raloxifene and aspirin without pre-extraction.
INADEQUATE (Incredible Natural Abundance DoublE QUAntum Transfer Experiment) is one of the most important techniques in revealing the carbon skeleton of organic solids in solid-state NMR spectroscopy. Nevertheless, its use for structural analysis is quite limited due to the low natural abundance of 13C–13C connectivity (∼0.01%) and thus low sensitivity. Particularly, in semi-solids like rubbers, the sensitivity will be further significantly reduced by the inefficient cross polarization from 1H to 13C due to molecular motions induced averaging of 1H–13C dipolar couplings. Herein, in this study, we demonstrate that transient nuclear Overhauser effect (NOE) can be used to efficiently enhance 13C signals, and thus enable rapid acquisition of two-dimensional (2D) 13C INADEQUATE spectra of rubbers. Using chlorobutyl rubber as the model system, it is found that an overall signal-to-noise ratio (SNR) enhancement about 22% can be achieved, leading to significant time-saving by about 33% as compared to the direct polarization-based INADEQUATE experiment. Further experimental results on natural rubber and ethylene propylene diene monomer (EPDM) rubber are also shown to demonstrate the robust performance of transient NOE enhanced INADEQUATE experiment.
Physical and theoretical chemistry, Analytical chemistry
Abstract This paper collects research information and registered data regarding the relationship between climate change and heritage, aiming to present a comprehensive state of studies and research on the subject. This relationship between these two cores is basically the main subject of this research, as well as the discovery of the areas with little information. Nowadays, there is a remarkable increase in the concern of the damage of cultural heritage and the research of methods and means of protection and of interpretation of its value. In the meanwhile, climate change is the other pillar of this paper, with evident damage, eminent jeopardy and accumulative downgrade of heritage assets. The aforementioned facts create a threatening background for the safeguarding of cultural and natural heritage and the transmission to the next generations. In general, stakeholders should focus on the mitigation of the human causes of climate change and the necessary adaptation to the climatic conditions for heritage protection. Through the collection of data, this paper presents the region of Mediterranean, as it has a strategic geographic location and the climatic conditions have already shown notable deviations. The presented information relates to the indices and measurements of the effects of climate change and the overall assessment of the risks of heritage, the irreversible impairment, the most common cultural aspects of the studies and the urgent need of protection. The scope of these data is the design of the appropriate management plan, taking into account the unique identity of each piece of heritage and its environment. To sum up, the kinds of heritage incorporated into the environment structuring a completed landscape with immediate exposure to the conditions, seem to lack the essential research for their preservation. For this reason, the adequate management of cultural and natural heritage in jeopardy, such as the cases in the Mediterranean region, require multidisciplinary assessment for heritage management.
Tudor Bibire, Daniel Vasile Timofte, Radu Dănilă
et al.
The topical therapy with rifampicin (RF)-based formulations is beneficial for treating postoperative wound infections and to accelerate healing. Despite recent research highlighting the antibiotic’s significant anti-inflammatory properties, limited topical wound healing products are currently available. The present study aimed to prove that the newly synthesized nanoparticles based on grafted alginate and poly(N-vinylcaprolactam) (pNVCL) and poly-lactic-co-glycolic acid (PLGA) contribute to the healing process of a wound. The methods used were at first the synthesis of the copolymer of alginate and pNVCL via grafting from technique and radical polymerization followed by water-in-oil-in water (W/O/W) emulsification; as oil phase PLGA dissolved in dichloromethane (DCM) was used. The formed nanoparticles were than characterized. The loaded RF was determined to be 160 µg/mL for a 20 mg formulation and within a four-hour time frame approximately 10% of the total loaded amount was released. The inhibitory concentrations (IC50) were 192.1 µg/mL for the nanoparticle, 208.8 µg/mL for pure rifampicin, and 718.1 µg/mL for the rifampicin-loaded nanoparticles. Considering the double role rifampicin was used for, the result was considered satisfactory in the way that these formulations could be used predominantly for postoperative wound irrigation in order to avoid infections and to improve healing.
Sooyoung Kim, Jae-Hwan Kwak, Jae-Kyung Jung
et al.
Abstract Objectives Carbon-14 (14C) labeling is a standard technology for tracing molecules and providing their pharmacokinetic profiles. However, its primary focus has been on small molecules, with limited application to biomacromolecules. Particularly in the development of new biological entities (NBE), the utilization of microdosing with a 14C-labeled biomacromolecule proves beneficial in the early stages of drug development, contributing to significant time and cost savings. This study investigates the 14C-labeling of antibody and explores the stability of 14C-labeled antibody under various storage conditions. Methods and results In this study, the utilization of 14C-formaldehyde for labeling target antibodies at various molar ratios revealed a direct correlation between labeling efficiency and the quantity of 14C-formaldehyde applied: 1.5 mol/mol for 14C-labeled antibody with the use of 10 equivalents of 14C-formaldehyde, 3.8 mol/mol for 14C-labeled antibody with the use of 10 equivalents of 14C-formaldehyde, and 10.5 mol/mol for 14C-labeled antibody with the use of 60 equivalents of 14C-formaldehyde. All the reaction conditions exhibited no antibody degradation, as evidenced by the absence of a significant change in HPLC purity compared to the unlabeled antibody. Stability tests revealed that all groups maintained their purities over a 4-week period at both − 75 ± 10 °C and 5 ± 3 °C. Given safety concerns related to internal radiation exposure in potential human subjects during microdosing, this study established optimal conditions for employing 14C-labeled antibodies. Therefore, it is optimized that 10 equivalents of 14C-formaldehyde can be used for 14C-antibody labeling through reductive amination, storing the antibodies at 5 ± 3 °C, and assigning a storage period of 4 weeks. Conclusion The findings from this study offer valuable insights into the effective application of 14C-labeling in microdosing studies, especially for larger molecules such as antibodies.
Asmaa A. Mandour, Nada Nabil, Hala E. Zaazaa
et al.
A comparative study between two stability-indicating chromatographic methods for the assay of brinzolamide and timolol maleate in the co-existence of the probable carcinogenic oxidative degradation product of timolol maleate in their ophthalmic formulation was demonstrated. The first method established the thin-layer chromatography coupled with the densitometric determination of the analyzed spots, using silica gel TLC aluminum plates F254 and a developing system of chloroform: methanol: ammonia (6:1:0.1, in volumes) at room temperature to give good separation for the three investigated components, where retardation factors for the oxidative degradation product of timolol maleate, brinzolamide and timolol maleate were (Rf 0.21), (Rf 0.46), and (Rf 0.55), respectively. The linear ranges were 2–10 and 3–16 μg/band for brinzolamide and timolol maleate, respectively. In the second method, high performance liquid chromatography (HPLC), photo diode array detection was used on a Eurospher 5 µm C18 100 Å (4.6 × 250 mm) column, using triethylamine pH 3.5, adjusted by glacial acetic acid: acetonitrile (20:80, <i>v/v</i>) at a rate of 0.5 mL per minute. An acceptable separation was achieved, where the retention times for timolol maleate, the oxidative degradation product of timolol maleate and brinzolamide, were (Rt 3.6), (Rt 4.7), and (Rt 5.6), respectively. Linearity covered a range of 20–120 μg/mL for both drugs. It has been proved previously that timolol maleate is liable to oxidation, giving a high-probability carcinogenic product in female mice. The validation for the new proposed stability-indicating methods was optimized in line with the ICH guidelines with good outcomes. It is worth noting that the HPLC-DAD method showed superior separation, economic and time-saving results, while TLC method was more sensitive.
Mohammadamin Tavakoli, Yin Ting T. Chiu, Alexander Shmakov
et al.
Deep learning-based reaction predictors have undergone significant architectural evolution. However, their reliance on reactions from the US Patent Office results in a lack of interpretable predictions and limited generalization capability to other chemistry domains, such as radical and atmospheric chemistry. To address these challenges, we introduce a new reaction predictor system, RMechRP, that leverages contrastive learning in conjunction with mechanistic pathways, the most interpretable representation of chemical reactions. Specifically designed for radical reactions, RMechRP provides different levels of interpretation of chemical reactions. We develop and train multiple deep-learning models using RMechDB, a public database of radical reactions, to establish the first benchmark for predicting radical reactions. Our results demonstrate the effectiveness of RMechRP in providing accurate and interpretable predictions of radical reactions, and its potential for various applications in atmospheric chemistry.
Despite the popularity of scaled harmonic frequency calculations in chemistry, sparse benchmarking is available to guide users on appropriate level of theory and basis set choices (model chemistry). Here, we assess the performance of over 600 model chemistries in scaled harmonic frequencies calculations evaluating different scaling factors types. We can summarise our results into three main findings: (1) using model chemistry-specific scaling factors optimised for three different frequency regions (low (below 1,000cm-1), mid (1,000-2,000cm-1), and high (above 2,000cm-1)) results in better agreement between the scaled harmonic and experimental frequencies compared to other choices; (2) larger basis sets and more robust levels of theory generally lead to superior performance; however, the particular model chemistry choice matters; and (3) outliers should be expected in routine calculations. In terms of specific recommendations, overall, the highest accuracy model chemistries are double-hybrid functionals with non-Pople augmented triple-zeta basis sets, which can produce median frequency errors of down to 7.6cm-1 (DSD-PBEP86/def2-TZVPD) lying close to the error in the harmonic approximation. Double-zeta basis sets should not be used with double-hybrid functionals as there is no improvement compared to hybrid functionals. Note that the 6-311G* and 6-311+G* bases perform like double-zeta basis sets for vibrational frequencies. After scaling, all studied hybrid functionals with non-Pople triple-zeta basis sets will produce median errors of less than 15cm-1, with the best result of 9.9cm-1 with B97-1/def2-TZVPD. Appropriate matching of double-zeta basis sets with hybrid functionals can produce high quality results. The B97-1, TPSS0-D3(BJ) or wB97X-D hybrid functionals with 6-31G*, pc-1 or pcseg-1 are recommended for fast routine calculations, all delivering median errors of 11-12cm-1.
Lien-Thuong Thi Nguyen, Ngoc-Hanh Thi Le, Hanh Kieu Thi Ta
et al.
Abstract Magnetic nanoparticles (MNPs) provide a fast, cost-effective, and organic-free method for DNA isolation. In this paper, we synthesized MNP coated with oleic acid (Fe3O4@OA) and silica nanoparticles (Fe3O4@OA@SiO2), characterized the properties of MNP using TEM, VSM, and FTIR, and investigated their efficiency in DNA isolation from cyanobacteria. The yield and quality of isolated DNA were evaluated and compared with those from animal blood and those obtained by the silica column or organic solvents. The results showed the successful preparations of Fe3O4@OA and Fe3O4@OA@SiO2 with superparamagnetic behaviors and a mean diameter of 7 nm and 106 nm, respectively. The FTIR spectra of Fe3O4@OA confirmed the bonding of OA to the surface of iron oxide, while those of Fe3O4@OA@SiO2 showed the exposed silanol groups. Although MNPs yielded a lower quantity of DNA compared with phenol/chloroform extraction, they showed the potential protection of the integrity of DNA against centrifugal and shear forces. Fe3O4@OA@SiO2 favored more nucleic acid absorption than Fe3O4@OA, producing a 1.2 and 1.6 times greater amount of DNA from Arthrospira platensis and animal blood respectively. The purity of DNA isolated from Arthrospira platensis was also higher than that of animal blood. These findings indicate a new and simple approach for the isolation of DNA from Arthrospira genus. Graphical Abstract
Abstract The Road of Tang Poetry in Eastern Zhejiang is a poetic cultural route linked by Tang poetry which is the pinnacle of ancient Chinese poetry history, and is a cluster of cultural landscapes where nature and humanity blend together under the narrative of Tang poetry. The research has mined and collated the text information of poems, such as trails, persons, places and landscapes, in 1593 poems written by 451 poets of the Tang Dynasty in Eastern Zhejiang, and discerned the overall route of the Road of Tang Poetry in Eastern Zhejiang based on the spatial location of all the text information in GIS. The spatial distribution pattern of the cultural landscape of the Road of Tang Poetry is analyzed and summarized from four levels: natural landscape, Buddhist and Taoist cultural landscape, celebrity cultural landscape and folk cultural landscape. The complex social network relationship between “poet-person” and “poet-landscape” is shown through the Gephi tools. The four causes and two characteristics of the Road of Tang poetry in Eastern Zhejiang are explained from the perspective of the logic of mathematical statistics.
The relative abundances of singly-deuterated methanol isotopologues, [CH$_{2}$DOH]/[CH$_{3}$OD], in star-forming regions deviate from the statistically expected ratio of 3. In Orion KL, the nearest high-mass star-forming region to Earth, the singly-deuterated methanol ratio is about 1, and the cause for this observation has been explored through theory for nearly three decades. We present high-angular resolution observations of Orion KL using the Atacama Large Millimeter/submillimeter Array to map small-scale changes in CH$_{3}$OD column density across the nebula, which provide a new avenue to examine the deuterium chemistry during star and planet formation. By considering how CH$_{3}$OD column densities vary with temperature, we find evidence of chemical processes that can significantly alter the observed column densities. The astronomical data are compared with existing theoretical work and support D-H exchange between CH$_{3}$OH and heavy water (i.e., HDO and D$_{2}$O) at methanol's hydroxyl site in the icy mantles of dust grains. The enhanced CH$_{3}$OD column densities are localized to the Hot Core-SW region, a pattern that may be linked to the coupled evolution of ice mantel chemistry and star formation in giant molecular clouds. This work provides new perspectives on deuterated methanol chemistry in Orion KL and informs considerations that may guide future theoretical, experimental, and observational work.
Jonathan Schwartz, Zichao Wendy Di, Yi Jiang
et al.
Efforts to map atomic-scale chemistry at low doses with minimal noise using electron microscopes are fundamentally limited by inelastic interactions. Here, fused multi-modal electron microscopy offers high signal-to-noise ratio (SNR) recovery of material chemistry at nano- and atomic- resolution by coupling correlated information encoded within both elastic scattering (high-angle annular dark field (HAADF)) and inelastic spectroscopic signals (electron energy loss (EELS) or energy-dispersive x-ray (EDX)). By linking these simultaneously acquired signals, or modalities, the chemical distribution within nanomaterials can be imaged at significantly lower doses with existing detector hardware. In many cases, the dose requirements can be reduced by over one order of magnitude. This high SNR recovery of chemistry is tested against simulated and experimental atomic resolution data of heterogeneous nanomaterials.