Molecular Physics Research Articles

Structural and theoretical exploration of a multi-methoxy chalcone: Synthesis, quantum theory, electrostatics, molecular packing, DFT analysis, and in-silico anti-cancer evaluation

This study explores the pharmacological potential of chalcones through a multidisciplinary approach, including synthesis, quantum theory, molecular electrostatics, and density functional theory (DFT) calculations. The synthesized compound, analyzed via single crystal X-ray diffraction, crystallized in the triclinic system (space group P-1) with C–H⋯O interactions stabilizing its structure. Hirshfeld surface analysis confirms these interactions, with H–H contacts dominating (45.1 %). Molecular electrostatics analysis reveals charge distribution, and a 3.10 eV HOMO-LUMO energy gap indicates bioactivity. Molecular docking identifies the compound (3a) showed a maximum Gscore of HTNF-α (−9.81 kcal/mol); Tubulin (−7.96 kcal/mol); COX2 (−7.88 kcal/mol), EGFR (−6.72 kcal/mol), and VEGFR1(-2.50 kcal/mol). Where compound (3c) showed maximum binding at the putative binding site with dock scores for VEGFR2 (−9.24 kcal/mol). This research not only advances molecular science but also holds promise for diverse applications, including drug design. The significance of this study lies in its comprehensive exploration of the pharmacological potential of chalcones using a multidisciplinary approach. Through the integration of synthesis, quantum theory, molecular electrostatics, and density functional theory (DFT) calculations, we have extensively explored the structural and biochemical characteristics of these compounds. This investigation has revealed valuable insights that have the potential to lead to significant advancements in the fields of molecular science and drug design. Moreover, the molecular docking studies shed light on the compound's interaction with various biological targets. The significant binding affinities observed for these targets underscore the potential therapeutic relevance of the synthesized compound in diverse disease conditions.

Differences in the aroma quality of large-leaf yellow tea subjected to different roasting methods

Roasting is a key process in the production of large-leaf yellow tea (LYT) and substantially affects the formation of its aroma. In order to investigate the effect of roasting method on the aroma of large-leaf yellow tea and to identify the potential causes. In this study, guided by molecular sensory science, the aroma components of charcoal-roasted, electric-roasted and drum-roasted LYTs were analyzed using headspace solid phase microextraction and solvent-assisted flavor evaporation in conjunction with gas chromatography-mass spectrometry, and the data were visualized and analyzed using SMICA, SPSS and Origin. The results of quantitative descriptive analysis revealed that rice crust, burnt, corn and floral aromas were significantly different between the three samples. The results of aroma extract dilution and odor activity value analyses revealed that 2,4,5-trimethyloxazole, 1-ethylpyrrole-2-carboxaldehyde, 2-ethyl-3,5-dimethylpyrazine, 3-ethyl-2,5-dimethylpyrazine, linalool, 2,3-diethyl-5-methylpyrazine, 3,5-diethyl-2-methylpyrazine, β-damascenone, and (E)-β-ionone were the main compounds responsible for differences in the aroma of LYT subjected to different roasting methods. Aroma recombination and addition experiments verified these findings. All in all, charcoal roasting enhances the rice crust and burnt aromas of LYT, and drum roasting facilitates the presentation of floral and corn aromas. This study provides a theoretical basis for the processing of high-quality LYT.

Bibliometric and visual analysis of immunisation associated with acute kidney injury from 2003 to 2023.

This study aims to conduct a detailed bibliometric and visual analysis of acute kidney injury (AKI) and immune-related research conducted over the past two decades, focusing on identifying emerging trends and key areas of interest. The Web of Science Core Collection (WoSCC) was utilised for the meticulous examination of various parameters including publication volume, authorship, geographic distribution, institutional contributions, journal sources, prevalent keywords and citation frequencies. Data were intricately visualised and interpreted using VOSviewer, CiteSpace and Excel 365 software. Analysis of the WoSCC database revealed 3,537 articles on AKI and immunisation, originating from 94 countries and regions, involving 3,552 institutions and authored by 18,243 individuals. Notably, the top five countries contributing to this field were the United States, China, Germany, Italy and the United Kingdom, with the United States leading with 35.76% of total publications. Among the 3,552 contributing institutions, those in the United States were predominant, with Harvard University leading with 134 papers and 3,906 citations. Key journals driving productivity included Frontiers in Immunology, Kidney International, Journal of the American Society of Nephrology and International Journal of Molecular Sciences, with Kidney International being the most cited, followed by Journal of the American Society of Nephrology and New England Journal of Medicine. Prominent authors in the field included Ronco Claudio, Okusa Mark D and Anders, Hans-Joachim. Co-citation clustering and timeline analysis highlighted recent research foci such as COVID-19, immune checkpoint inhibitors, regulated necrosis, cirrhosis and AKI. Keyword analysis identified "inflammation," "ischaemia-reperfusion injury," "sepsis," "covid-19," and "oxidative stress" as prevalent terms. This study provides the first bibliometric analysis of AKI and immune research, offering a comprehensive overview of research hotspots and evolving trends within the field.

Integrating Computational Methods into Antibacterial Drug Discovery and Development from Natural Products

Natural products have long been pivotal in sustaining civilizations due to their medicinal properties and have served as a rich source of bioactive compounds for drug discovery. With the rise of antibiotic-resistant bacteria, there is an urgent need for new antibacterial agents. Natural products, with their diverse chemical structures, provide a promising reservoir for identifying new lead compounds. Historically, the discovery of bioactive natural products often relied on serendipity, but modern advancements in computational approaches, particularly computer-aided drug design (CADD), have revolutionized this process. In the modern era, vast data from advanced technologies can provide valuable insights through computational methods. These approaches enable the structural analysis of molecules and the prediction of their biological activities, accelerating drug discovery. Advances in molecular sciences have identified more antibacterial targets, further facilitating this process. Integrating computational drug design with the study of natural products allows for the efficient identification and optimization of potential antibacterial agents. Moreover, many medicinal plants harbor mechanisms of action that remain unexplored by conventional methods. By employing computational techniques, researchers can uncover these mechanisms and develop novel antibacterial drugs. This combined approach not only enhances our understanding of natural products but also addresses the critical need for new treatments in the fight against bacterial infections.

DETERMINING THE DENSITY AND MOLAR MASS OF AIR IN A HOME EXPERIMENT

Formulation of the problem. Experimental research is an integral part of physics education. During distance learning, students can carry out hands-on experiments only at home. Modern smartphones, equipped with various sensors, offer significant capabilities for this purpose. The literature offers quite extensive descriptions of experiments aimed at determining mechanical, acoustic, and optical quantities using smartphones. At the same time, insufficient attention has been paid to determining gas parameters that can be measured using the pressure sensor embedded in smartphones. Therefore, the relevant task is to develop a methodology for experimenting to determine the density of air and its molar mass at home using a pressure sensor. Materials and methods. To achieve the objective of the study, we used the analysis of the curriculum of the course "General Physics for Bachelor of Engineering", a review of the methodological instructions for performing laboratory work in the section "Molecular Physics and Thermodynamics" of the physics course of technical universities, a review of the literature on the topic of the study, and an analysis of the results of student research on the dependence of air pressure on altitude. We also surveyed students about the possibility of conducting the research at home and their interest in conducting other experiments using a smartphone. Results. The methodology for determining the density and molar mass of air was developed based on the results of a study of the pressure-height dependence. It is shown that it is necessary to perform statistical processing of experimental data to estimate the sought quantities. The experimental results allowed us to obtain values of density and molar mass of air that show a good correlation with the tabulated values. Conclusions. Studying the pressure-altitude relationship using a smartphone and the PhyPhox application allows for fairly accurate calculations of air density and molar mass. According to the survey results, students responded positively to conducting home experiments using smartphones.

A recommended line list for water vapor in the 12,969–13,418cm-1 interval

We have recently devoted two reports to the very weak absorption spectrum of water vapor in the 12,969 – 13,417 cm-1 region by high sensitivity cavity ring down spectroscopy (CRDS) [Vasilchenko et al. J. Quant. Spectrosc. Radiat. Transfer 275 (2021) 107,847; doi.org/10.1016/j.jqsrt.2021.107847; Vasilchenko et al. Molecular Physics e2051762; doi.org/10.1080/00,268,976.2022.2051762]. This spectral interval is important because it includes the region of the oxygen A-band near 760 nm. The achieved sensitivity allowed us to measure lines with intensity on the order of 10–29 cm molecule-1, about two orders of magnitude lower than the detectivity threshold of previous studies. A total of about 240 energy levels of H216O were newly determined. Our comparison to the W2020 empirical levels [Furtenbacher et al. J. Phys. Chem. Ref. Data 49 (2020) 043,103; doi.org/10.1063/5.0030680] led us to identify and correct about 300 W2020 energy levels of the main isotopologue differing from our energy value by more than 5 × 10–3 cm-1. In the present contribution, we consider in details the sources of the W2020 energy levels to identify the origin of these deviations. We confirm that more than 260 energy levels should be corrected but for the remaining thirty-two levels, the W2020 energy values are in fact, more reliable. As a result, we propose an improved list of energy levels retrieved from the CRDS data and a recommended line list for water vapor in natural isotopic abundance in the 12,969 – 13,417 cm-1 region, mostly based on the CRDS line parameters.

Theory vs. experiment: The rise of the dynamic view of proteins

Over the past century, the scientific conception of the protein has evolved significantly. This paper focuses on the most recent stage of this evolution, namely, the origin of the dynamic view of proteins and the challenge it posed to the static view of classical molecular biology. Philosophers and scientists have offered two hypotheses to explain the origin of the dynamic view and its slow reception by structural biologists. Some have argued that the shift from the static to the dynamic view was a Kuhnian revolution, driven by the accumulation of dynamic anomalies, while others have argued that the shift was caused by new empirical findings made possible by technological advances. I analyze this scientific episode and ultimately reject both of these empiricist accounts. I argue that focusing primarily on technological advances and empirical discoveries overlooks the important role of theory in driving this scientific change. I show how the application of general thermodynamic principles to proteins gave rise to the dynamic view, and a commitment to these principles then led early adopters to seek out the empirical examples of protein dynamics, which would eventually convince their peers. My analysis of this historical case shows that empiricist accounts of modern scientific progress—at least those that aim to explain developments in the molecular life sciences—need to be tempered in order to capture the interplay between theory and experiment.

Versatile Chip-Scale Lasers : Bridging Near-Ultraviolet to Near-Infrared Spectra

Narrow-linewidth lasers that are widely tunable in the visible spectrum are crucial for various applications such as quantum optics, optical clocks, and atomic and molecular physics. However, current laser systems are typically bulky and confined to laboratory settings, limiting their practical use beyond research environments. In this study, we introduce a chip-scale visible laser platform capable of producing tunable and narrow-linewidth lasers spanning from near-ultraviolet to near-infrared wavelengths. By leveraging micrometer-scale silicon nitride resonators and off-the-shelf Fabry–Pérot laser diodes, we achieve significant coarse tuning capabilities of up to 12.5 nm, coupled with mode-hop-free fine tuning up to 33.9 GHz. Remarkably, our lasers exhibit intrinsic linewidths as low as a few kilohertz. Additionally, our platform demonstrates impressive fine-tuning speeds of up to 267 GHz per microsecond, alongside fiber-coupled powers reaching up to 10 mW and typical side-mode suppression ratios surpassing 35 dB. These remarkable specifications of our chip-scale lasers rival those previously attainable only with large, state-of-the-art benchtop laser systems. This breakthrough positions our lasers as powerful tools poised to drive the next generation of visible-light technologies, enabling practical applications in various fields beyond the confines of traditional laboratory setups.

Comparative investigation on the aroma profiles of edible citrus flowers in the main organs and different developmental stages

Pomelo flowers emit a strong fragrance and give aromatic odors. Volatile compounds from pomelo flowers were analyzed at three developmental stages and in the main organs by molecular sensory science. A total of 134 volatiles including 25 odorants, were analyzed by gas chromatography–mass spectrometry/pulsed flame photometric detector (GC–MS/PFPD) and multidimensional GC–MS/olfactory (MDGC–MS/O). The total volatile content varied among pomelo flowers at different developmental stages (stage-III > stage-II > stage-I) and among different organs of pomelo flowers (petal > pistil > stamen). Linalool was an important odorant with a high OAV, and floral/fruity comprised the predominant aroma profile. Four odorants, ethyl 2-methylbutanoate, linalool, β-myrcene, and 2-butenal, were selected based on variable importance in projection (VIP) values and contributed mainly to the discrimination of pomelo flowers at three different developmental stages. Linalool, β-myrcene, d-limonene, and ethyl hexanoate were potential markers for evaluating flavor differences in pomelo floral organs.

New line list for the ν4 bands of the trans (790.117 cm–1) and cis (851.943 cm–1) conformers of nitrous acid (HONO): Accurate positions and absolute intensities

The goal of this work was to update and significantly improve the line lists that have been generated recently for 11 µm bands of the trans- and cis- conformer forms of nitrous acid (HONO) [Armante R, Perrin A, Kwabia Tchana F, Manceron L. The ν4 bands at 11 μm: linelists for the trans- and cis- conformer forms of nitrous acid (HONO) in the 2019 version of the GEISA database. Molecular Physics 2021;120:e1951860]. That 2019 version of the 11 µm line list was generated using the spectroscopic parameters that were available, at that time, in the literature. During the present study, we used high-resolution Fourier transform spectra recorded at 11 µm to perform a large investigation of line positions and intensities for the ν4 bands of the trans- and cis-conformer of HONO. The resulting set of experimental ν4 (absolute) intensities and of 41 energy levels were used to determine, by least squares fit computations, improved position and intensity parameters for the ν4 bands of the trans- and cis-conformer of HONO. For trans-HONO, the ν4 band appeared not to be perturbed, while for cis-HONO a weak high order B-type Coriolis, coupling together the 41 and 61 energy levels was evidenced for the first time. This new list is of potential interest for the IASI-NG (Infrared Atmospheric Sounding Interferometer - New Generation) instrument which will be launched on board the METOP-SG satellite in 2025.

Exploring microbial and moist-heat effects on Pu-erh tea volatiles and understanding the methoxybenzene formation mechanism using molecular sensory science

Piling fermentation (PF) is crucial for Pu-erh tea aroma, yet its microbial and moist-heat impact on aroma quality is poorly understood. Solid-phase microextraction, solvent-assisted flavor evaporation, and gas chromatography–mass spectrometry were used to detected and analyses the samples of sun-green green tea, sterile PF and spontaneous PF. Microbiological action promotes the formation of stale aromas. Moist-heat action promotes the formation of plum-fragrance and sweet aroma. 20 microbial markers and 28 moist-heat markers were screened from 184 volatile components. Combining odor activity values and gas chromatography-olfactometry, 22 aroma-active compounds were screened (1,2,3-trimethoxybenzene, linalool, 1,2,4-trimethoxybenzene …), and analyzed during PF processing. Aroma omission and addition experiments verified its importance. Gallic acid addition experiments successfully verified that microorganisms are the main contributors to the synthesis of methoxybenzenes. Finally, Blastobotrys, Rasamsonia, and Thermomyces showed positive correlation with the synthesis of 1-ethyl-4-methoxybenzene, 1,2,4-trimethoxybenzene, 1,2,3-trimethoxybenzene, and 1,2-dimethoxybenzene. The formation mechanism of Pu-erh tea's aroma was clarified.Exploring microbial and moist-heat effects on Pu-erh tea volatiles and understanding the methoxybenzene formation mechanism using molecular sensory science.

Special issue of J. Magn. Magn. Mater., “Physics of Magnetism 2023 – Special issue in memory of professor Roman Micnas”, consisting of articles presented at The European conference Physics of Magnetism 2023: In memory of Professor Roman Micnas

The European Conference PHYSICS OF MAGNETISM 2023 (PM’23) was held on June 26–30, 2023 in Poznań, Poland. It was the 17th in a series of conferences organized by the Faculty of Physics of the Adam Mickiewicz University and the Institute of Molecular Physics of the Polish Academy of Sciences. The PM’23 conference was dedicated to the memory of Professor Roman Micnas, a long–time co-organizer of the conference, and its co-chairman since 1993. The preface presents basic information about the topics and events related to the PM’23 conference.

SDD Spectral Radii and SDD Energies of Graph Operations

Graph energies and spectral radii have application in molecular computing and computer sciences. In this paper, we concentrate on new findings about the Symmetric Division Deg, (SDD) energies, and (SDD) spectral radii of p splitting and p shadow graphs built on the foundation of any regular graph. In fact it becomes natural to ask how the SDD energies and spectral radii of newly formed graphs depend on the SDD energies and spectral radii of the given regular graph.

Gold-catalyzed Reactions of Substituted 1,5-diynes: Recent Advances and their Chemistry

Abstract: Diynes are identified as exceptionally potent and superior substrates in gold-catalyzed organic transformations. Gold (I) and gold (III) complexes exhibit unique activity towards diynes, encouraging the nucleophilic addition of different functional groups both inter and intra- molecularly. In this review, particularly, we focused on recent advances in gold-catalyzed reactions of 1,5-diynes along with their mechanistic aspects. These reactions are interesting for constructing molecular complexity, medicinal chemistry, and material science.

Characterization of key aroma-active compounds in fresh and vacuum freeze-drying mulberry by molecular sensory science methods

Mulberry is prone to rapid deterioration, but its quality can be maintained through vacuum freeze-drying. In this study, the aroma compositions of fresh mulberry (FM) and vacuum freeze-dried mulberry (VFDM) were analyzed through headspace solid-phase microextraction (HS-SPME) and solvent-assisted flavor evaporation (SAFE) coupled with GC×GC–O–TOF-MS. A total of 232 volatiles were detected in FM and VFDM, and the content of volatile compounds in VFDM decreased by at least 21.37 % after drying compared to FM. Additionally, 51 and 50 aroma-active compounds were detected in FM and VFDM, respectively, with 13 aroma-active compounds being identified in FM initially. Based on the aroma extraction dilution analysis (AEDA) results, 14 compounds with high flavor dilution (FD) factors were accurately quantified by GC–MS. The calculated odor activity value (OAV) showed that a total of 12 compounds significantly contributed to the aroma of mulberry. Finally, aroma recombination and omission experimental results showed that (E,Z)-2,6-nonadienal, β-ionone, hexanal, and (E)-2-nonenal were the key aroma-active compounds in FM, whereas (E,Z)-2,6-nonadienal, β-ionone, (E)-2-nonenal, eugenol and ethyl isovalerate were the key aroma-active compounds in VFDM.

Research status and hotspots in the field of endoplasmic reticulum stress and liver disease: A bibliometric study.

Recently, the study of endoplasmic reticulum stress (ERS) and liver disease has attracted much attention, but bibliometric analysis on this field is scarce. Therefore, to address this gap, we conducted a bibliometric analysis to explore the research status, hotspots, and trends in this field. We searched the Web of Science Core Collection database for publications on ERS and liver disease from 2007 to 2022. Bibliometric online analysis platform, VOSviewer, and CiteSpace were used to perform bibliometric analysis. Two thousand seven hundred fifty-one publications were retrieved form the Web of Science Core Collection database. The USA was the most productive and influential country. Seoul National University, International Journal of Molecular Sciences, and Kaufman RJ were the most productive institution, journal, and author. "Endoplasmic reticulum stress," "nonalcoholic fatty liver disease," "inflammation," "oxidative stress" and "insulin resistance" were the high-frequency keywords, "necrosis factor alpha" was the keywords with the strongest citation bursts, and "nonalcoholic fatty liver," "fibrosis" and "lipid droplet" were the keywords that were still bursting in 2022. The number of publications on ERS and liver disease has increased over the past years. The USA was the most productive and influential country. China has become the country with the largest number of annual publications, but it still needs to work on the quality. ERS and nonalcoholic fatty liver disease, especially the insulin resistance and lipotoxicity in hepatocytes may be the research hotspots and trends in this field of ERS and liver disease.

ChARpack: The Chemistry Augmented Reality Package.

Off-loading visualization and interaction into virtual reality (VR) using head-mounted displays (HMDs) has gained considerable popularity in simulation sciences, particularly in chemical modeling. Because of its unique way of soft immersion, augmented reality (AR) HMD technology has even more potential to be integrated into the everyday workflow of computational chemists. In this work, we present our environment to explore the prospects of AR in chemistry and general molecular sciences: The chemistry in Augmented Reality package (chARpack). Besides providing an extensible framework, our software focuses on a seamless transition between a 3D stereoscopic view with true 3D interactions and the traditional desktop PC setup to provide users with the best setup for all tasks in their workflow. Using feedback from domain experts, we discuss our design requirements for this kind of hybrid working environment (AR + PC), regarding input, features, degree of immersion, and collaboration.

Alignment of ND3 molecules in dc-electric fields.

The control of movement and orientation of gas-phase molecules has become the focus of many research areas in molecular physics. Here, ND3 molecules are polarized in a segmented, curved electrostatic guide and adiabatically aligned inside a rotatable mass spectrometer (MS). Alignment is probed by photoionization using a linearly polarized laser. Rotation of the polarization at fixed MS orientation has the same effect as the rotation of the MS at fixed polarization, proving that the molecular alignment adiabatically follows the MS axis. Polarization-dependent ion signals reveal state-specific populations and allow for a quantification of the aligned sample in the space-fixed reference frame.

Characterization of Key Odor-Active Compounds in Draft Beers for the Chinese Market Using Molecular Sensory Science Approaches.

Beer is a popular alcoholic beverage worldwide. However, limited research has been conducted on identifying key odor-active components in lager-type draft beers for the Chinese market. Therefore, this study aims to elucidate the odor characteristics of the four most popular draft beer brands through a sensory evaluation and an electronic nose. Subsequently, the four draft beers were analyzed through solid-phase microextraction and liquid-liquid extraction using a two-dimensional comprehensive gas chromatography-olfactometry-mass spectrometry analysis (GC×GC-O-MS). Fifty-five volatile odor compounds were detected through GC×GC-O-MS. Through an Aroma Extract Dilution Analysis, 22 key odor-active compounds with flavor dilution factors ≥ 16 were identified, with 11 compounds having odor activity values > one. An electronic nose analysis revealed significant disparities in the odor characteristics of the four samples, enabling their distinct identification. These findings help us to better understand the flavor characteristics of draft beer and the stylistic differences between different brands of products and provide a theoretical basis for objectively evaluating the quality differences between different brands of draft beer.

Full spectroscopic model and trihybrid experimental-perturbative-variational line list for NH

ABSTRACT Imidogen (NH) is a reactive molecule whose presence in astrochemical environments is of interest due to its role in the formation of nitrogen-containing molecules and as a potential probe of nitrogen abundance. Spectroscopic NH monitoring is useful for Earth-based combustion and photolysis processes of ammonia and other nitrogen-containing species. NH is also relevant to ultracold molecular physics and plasma studies. To enable these diverse applications, high-quality molecular spectroscopic data are required. Here, a new line list with significant advantages over existing data is presented. Most notably, this line list models isotopologue spectroscopy and forbidden transitions (important for NH visible absorption), alongside some overall improvements to accuracy and completeness. This approach takes advantage of existing experimental data (from a previous MARVEL compilation) and perturbative line lists together with new MRCI ab initio electronic data. These are used to produce a novel variational spectroscopic model and trihybrid line list for the main 14N1H isotopologue, as well as isotopologue-extrapolated hybrid line lists for the 14N2H, 15N1H, and 15N2H isotopologues. The new 14N1H ExoMol-style trihybrid line list, kNigHt, comprises 4076 energy levels (1078 experimental) and 327 014 transitions up to 47 500 cm−1 (211 nm) between five low-lying electronic states (X 3Σ−, a 1Δ, b 1Σ+, A 3Π, and c 1Π). For most anticipated applications aside from far-infrared studies, this line list will be of sufficient quality; any improvements should focus on the b 1Σ+ energies, and the a 1Δ – A 3Π and b 1Σ+ – A 3Π spin–orbit couplings.