Chemical Research Research Articles

Computational aspects of DFT, HOMO-LUMO, PED, molecular docking and basic characterisations of Octadec-9-Enoic Acid (C18H34O2)

Finding a few potential ‘green’ inhibitors has been a long-term goal because these products that are derived from plants enable prescription drug costs reduced, side effects minimised and biodegradable. Known by its common name, Hybanthusenneaspermus (L.) F. Muell, which is a member of the Violaceae family, is a herb or shrub found worldwide in tropical and subtropical climates. Knowing the applicability of H. enneaspermus for the treatment of a variety of acute or chronic diseases with a diverse nature of phytoconstituents will be made easier with the information provided in this comprehensive article. The majority of the information in this research article was gathered from different scientific sources that focused on H. enneaspermus research. Plant extraction, optimised geometry, thorough vibrational assignment, and characterisation of the fundamental vibrational modes of Octadec-9-Enoic Acid were conducted using experimental FT-IR and UV-Vis data in addition to quantum chemistry research. The actual vibrational data were compared to the wavenumbers computed theoretically for the chemical's optimal shape using DFT/B3LYP gradient calculations with the 6-311G ++ (d,p) basis set. A computation has been performed utilising the energy gap between HOMO and LUMO. Intramolecular interactions (NBO), molecular electrostatic potential (MEP) at a specific point p (x,y,z), atomic charge values, NMR & UV-vis computation, and molecular docking studies with protein-ligand interactions were all interpreted using natural bond orbital analysis.

Values Are More Than Statements: Connecting Actions to Values to Build Inclusive Cultures in Chemistry Research Groups

Values Are More Than Statements: Connecting Actions to Values to Build Inclusive Cultures in Chemistry Research Groups

Nitrite facilitated transformation of halophenols in ice

This study investigated the expediated transformation of halophenols in the presence of nitrite (NO2−) under slightly acidic conditions in ice, whereas such transformation was negligible in liquid water at 4 °C. We proposed that this phenomenon was attributed to the freeze-concentration effect, incurring a pH drop and the aggregation of NO2− and halophenols within the liquid-like grain boundary layer amid ice crystals. Within this micro-environment, NO2− underwent protonation to generate reactive nitrous acid (HNO2) and nitrosonium ions (NO+) that facilitate the nitration and oxidation of halophenols. When 10 μМ halophenol was treated by freezing in the presence of 5 μМ NO2−, the total yields of nitrated products reached 2.4 μМ and 1.4 μМ within 12 h for 2-chlorophenol (2CP) and 2-bromophenol (2BP), respectively. NO+ drove oxidative coupling reactions, generating hydroxyl polyhalogenated diphenyl ethers (OH-PBDEs) and hydroxyl polyhalogenated diphenyls via C-O or C-C coupling. These two pathways were intricately intertwined. The presence of natural organic matter (NOM) mitigated the formation of nitrated products and completely suppressed the coupling products. This study offers valuable insights into the fate of halophenols in ice and suggests potential pathways for the formation of nitrophenolic compounds and OH-PBDEs in natural cold environments. These findings also open up a new avenue in environmental chemistry research.

ChemReco: automated recognition of hand-drawn carbon–hydrogen–oxygen structures using deep learning

Chemical molecular structures are a direct and convenient means of expressing chemical knowledge, playing a vital role in academic communication. In chemistry, hand drawing is a common task for students and researchers. If we can convert hand-drawn chemical molecular structures into machine-readable formats, like SMILES encoding, computers can efficiently process and analyze these structures, significantly enhancing the efficiency of chemical research. Furthermore, with the progress of educational technology, automated grading is gaining popularity. When machines automatically recognize chemical molecular structures and assess the correctness of the drawings, it offers great convenience to teachers. We created ChemReco, a tool designed to identify chemical molecular structures involving three atoms: C, H, and O, providing convenience for chemical researchers. Currently, there are limited studies on hand-drawn chemical molecular structures. Therefore, the primary focus of this paper is constructing datasets. We propose a synthetic image method to rapidly generate images resembling hand-drawn chemical molecular structures, enhancing dataset acquisition efficiency. Regarding model selection, the hand-drawn chemical molecule structural recognition model developed in this article achieves a final recognition accuracy of 96.90%. This model employs the encoder-decoder architecture of EfficientNet + Transformer, demonstrating superior performance compared to other encoder-decoder combinations.

Resolving the current controversy of use and reuse of housekeeping proteins in ageing research: Focus on saving people’s tax dollars

The use of housekeeping genes and proteins to normalize mRNA and protein levels in biomedical research has faced growing scrutiny. Researchers encounter challenges in determining the optimal frequency for running housekeeping proteins such as β-actin, Tubulin, and GAPDH for nuclear-encoded proteins, and Porin, HSP60, and TOM20 for mitochondrial proteins alongside experimental proteins. The regulation of these proteins varies with age, gender, disease progression, epitope nature, gel running conditions, and their reported sizes can differ among antibody suppliers. Additionally, anonymous readers have raised concerns about peer-reviewed and published articles, creating confusion and concern within the research and academic institutions. To clarify these matters, this minireview discusses the role of reference housekeeping proteins in Western blot analysis and outlines key considerations for their use as normalization controls. Instead of Western blotting of housekeeping proteins, staining of total proteins, using Amido Black and Coomassie Blue can be visualized the total protein content on a membrane. The reducing repeated Western blotting analysis of housekeeping proteins, will save resources, time and efforts and in turn increase the number of competitive grants from NIH and funding agencies. We also discussed the use of dot blots over traditional Western blots, when protein levels are low in rare tissues/specimens and cell lines. We sincerely hope that the facts, figures, and discussions presented in this article will clarify the current controversy regarding housekeeping protein(s) use, reuse, and functional aspects of housekeeping proteins. The contents presented in our article will be useful to students, scholars and researchers of all levels in cell biology, protein chemistry and mitochondrial research.

Fragment Aligned Molecular Orbital Analysis: An Innovative Tool for Analyzing Atypical Chemical Bonding.

In chemical research, it is a common practice to carry out quantum chemical calculations and analyze the canonical molecular orbitals (CMOs) obtained to study electronic structures of chemical systems. However, extensive orbital mixing of CMOs especially in molecular clusters significantly complicates our understanding of the electronic structures. In this paper, we have developed an innovative tool called fragment aligned molecular orbital (FAMO) analysis, which reconstructs our modular chemical picture by making use of the Procrustes analysis in statistical theory to align the occupied molecular orbitals of a molecular species against the occupied (molecular) orbitals of the constituting fragments of the cluster, and results in a set of chemically intuitive semilocalized orbitals. This alignment technique minimizes the extensive orbital mixing, thus allowing precise observation of bonding interactions in complex chemical systems. A few representative clusters have been selected as showcase examples to demonstrate the advantage of FAMO analysis in deciphering the distinct bonding interactions in cluster compounds.

Holistic analysis of a gliding arc discharge using 3D tomography and single-shot fluorescence lifetime imaging

Gliding arc plasmas, a versatile form of non-thermal plasma discharges, hold great promise for sustainable chemical conversion in electrified industrial applications. Their relatively high temperatures compared to other non-thermal plasmas, reactive species generation, and efficient energy transfer make them ideal for an energy-efficient society. However, plasma discharges are transient and complex 3D entities influenced by gas pressure, mixture, and power, posing challenges for in-situ measurements of chemical species and spatial dynamics. Here we demonstrate a combination of innovative approaches, providing a comprehensive view of discharges and their chemical surroundings by combining fluorescence lifetime imaging of hydroxyl (OH) radicals with optical emission 3D tomography. This reveals variations in OH radical distributions under different conditions and local variations in fluorescence quantum yield with high spatial resolution from a single laser shot. Our results and methodology offer a multidimensional platform for interdisciplinary research in plasma physics and chemistry.

Efficient trust region filter modeling strategies for computationally expensive black-box optimization

The study and application of contemporary optimization techniques considerably enhance the efficiency of chemical research and manufacturing. With the dynamic progression of modern manufacturing technologies, the emergence of numerous black-box models characterized by inaccessible mathematical formulations and high evaluation costs poses new challenges to traditional optimization methods, leading to difficulty in programming and solving. Hence, based on the trust region filter (TRF) method, we define a new framework to elevate optimization efficiency in this study for chemical systems involving computationally expensive black-box functions. Sampling size per iteration is reduced, and sampling efficiency is improved by incorporating the known data beyond the trust region to assist in constructing reduced models, which is achieved by the application of the Gaussian process. Through comparison and validation of benchmark tests and case studies, this approach demonstrates that using the Gaussian process as the reduced model can lower the number of calls to black-box functions by more than half compared to common linear and quadratic models, and convergence to first-order critical points can still be guaranteed.

Reflections in Chemical Safety and Research: Doing Science Against All Odds in the Philippines

Reflections in Chemical Safety and Research: Doing Science Against All Odds in the Philippines

Development of LC-MS/MS method for quantification of Lurasidone using volumetric absorptive microsampling (VAMS); a comparative study between dried blood and plasma samples

The ecological impact of biological, chemical, and analytical research practices, including toxic reagents and biohazardous waste, has led to the development of alternative sampling and extraction techniques for bioanalysis. Microsampling (sample volume < 50 µL) aligns with the 3Rs principle, allowing multiple sampling points from the same animal at different time points and improving animal welfare. A bioanalytical method was developed to investigate factors related to bioanalytical challenges and the implementation of microsampling techniques. An LC-MS/MS method for Volumetric Absorptive Microsampling (VAMS), 20 µL, was developed for quantifying Lurasidone using a liquid–liquid extraction technique. The method uses a C18, Phenomenex column for chromatographic separation and a mobile phase composition of Methanol, Acetonitrile, and Water with 0.1 % HFBA. The method was validated over a concentration range of 5.0 to 1200.0 ng/mL and achieved acceptable precision and accuracy. The recovery for analyte from VAMS was approximately 40% at four different concentrations and is consistent (%CV < 15), with no significant differences among HCT levels. The matrix factor ranged between 85.00 and 115.00 %, showing no substantial issues with reduced or enhanced signal. The stability data showed no significant degradation of LUR in VAMS samples when stored at room temperature for 15 days. The newly established method for Lurasidone confirmed the use of VAMS sampling method and its analysis on LC-MS/MS. Further, the data obtained from microsampling techniques was compared with conventional (plasma) technique, as proof-of-concept, and it confirms the agreement between the two methods. The study supports the advantages of microsampling in protecting the environment and animals while maintaining scientific judgement.

Interactions of Clay Minerals with Biomolecules and Protocells Complex Structures in the Origin of Life: A Review

AbstractThe origin of life (OoL) has always been a mysterious and challenging topic that puzzles human beings. Clay minerals have unique properties and wide distribution in early Earth environments. They can not only adsorb biological small molecules to catalyze their polymerization, but play an active role in the formation and evolution of protocells. In this review, the research progress on the interactions of clay minerals with biomolecules and protocells complex structures in the field of the OoL based on chemical evolution theory is summarized. The types, structures and properties of clay minerals, biological molecules and protocell models related to the OoL are introduced in detail. The mechanism of interaction between clay minerals and biological molecules, the construction of protocells and the role of clay minerals in the formation, structure and stability of protocells are systematically described. Finally, the future research priorities and challenges in the field of OoL based on clay minerals, biomolecules and protocells are discussed. It is aspired that this review can further advance the exploration of the OoL from a new perspective, and can also bring some interesting findings and ideas to the interdisciplinary research of materials, biology, chemistry and other related disciplines.Clay minerals have a variety of interactions with small biomolecules, which can be used as structural and functional templates to promote the organic synthesis of biomolecules and the formation and evolution of protocells, playing a non‐negligible role in the field of the OoL.

Investigating empirical and theoretical calculations for intensity ratios of L-Shell X-ray transitions in atoms with 39 ≤ Z ≤ 94

The significance of theoretical, experimental, and analytical methods in calculating the intensity ratios of L-shell transitions for diverse elements lies in their widespread applications across various domains, including physical chemistry and medical research. In the present paper, empirical values for intensity ratios were computed through polynomial interpolations using experimental databases within the scope of atomic number 39 ≤ Z ≤ 92 for ILβILα and ILγILα, and extending to the range of 39 ≤ Z ≤ 94 for ILlILα. Additionally, new theoretical calculations were conducted using the Multiconfiguration Dirac–Fock Method for specific elements. The obtained results were compared with standard theoretical, experimental, and empirical values, showing a reasonable agreement with them.

Supramolecular chemistry in cyclodextrin inclusion complexes: The formation rules of terpenes/β-cyclodextrin inclusion complexes

Supramolecular chemistry of cyclodextrins (CDs) inclusion complexes is a hot research topic at present, but current studies often focus on the host-guest interaction between CDs and hydrophobic substances, while ignoring the self-assembly behavior of the host and guest during the inclusion process. Based on the spatial structures, six representative terpenes were selected in this study, and the stoichiometric ratio between terpenes and β-cyclodextrin (β-CD) was investigated by isothermal titration calorimetry (ITC) method. Meanwhile, the constructed inclusion complexes (ICs) were characterized by nuclear magnetic resonance, X-ray diffraction, scanning electron microscope, etc. On this basis, the assembly process of β-CD and terpenes was investigated firstly by molecular simulation method, and the inclusion process between β-CD and terpenes was further studied in terms of the formation of individual ICs and ICs aggregates. Results showed that hydrophobic interaction and van der Waals force were the main driving forces of the reaction between terpenes and β-CD, and the formation of ICs, β-CD molecule aggregation, terpene aggregation, and ICs aggregation occurred simultaneously during the inclusion process of terpenes and β-CD. To sum up, this study may provide certain thinking and reference for the subsequent supramolecular chemical research on CDs.

On Perceiving Molecular Time: Computational Chemical Simulations and the Moving Image

The perception of time undergoes a radical shift between the human scale and the nanoscale. In an age of rapidly evolving media and scientific technologies, we need to understand how these impact human perception and visual culture. This essay explores computational molecular simulations through the lenses of temporal media theory and moving image practice. Emerging from a creative fellowship with a physical chemistry research group, I focus on two moving image works that depict crystalline structures. One is a nanoscale computational simulation of soot formation and the other is a durational video artwork showing the dissolution of sugar. Computational molecular simulations are shown to produce a feeling of time by smearing an extremely short duration across a longer perceptible duration. This analysis uncovers how the awareness of media as a construct troubles our chronoception (perception of time), while unexpectedly, the screen becomes complicit in scientists’ expert temporal understanding. The videos present vastly different spatial and temporal scales and have different chronoceptive effects: one gives a sense of being within time, the other across time. Ultimately, computational simulations emerge as isomorphic media that have explicit aesthetic properties that connect us to the implicit, abstract energetics of chemical reactivity.

Response of NPK and Neem Cake on Soil Properties, Growth and Yield of Cluster Bean

At the soil science and agricultural chemistry research farm, an experiment was carried out during the 2023–2024 growing season. Nine treatments were arranged in a randomised block design with three replications for the current investigations. The pre-sowing soil sample used for the analysis of the cluster bean was taken for the study. The soil has a sandy loam texture, and the cluster bean responds considerably to the various treatment combinations. Under treatment T9 -, the highest phosphorus was measured at 30.43 kg ha-1 in 0–15 cm deep and 27.65 kg ha-1 in 15–30 cm depth. and in treatment T1, the lowest phosphorus levels were 18.81 kg ha-1 at 0–15 cm depth and 15.74 kg ha-1 at 15–30 cm depth. Treatment T9 produced the highest potassium levels, 252.9 kg ha-1 in 0–15 cm depth and 186.7 kg ha-1 in 15–30 cm depth, while treatment T1 produced the lowest potassium levels, 199.7 kg ha-1 in 0–15 cm depth and 166.8 kg ha-1 in 15–30 cm depth.

Celebrating 40 Years of Chemical Research in Chinese Universities

Celebrating 40 Years of Chemical Research in Chinese Universities

Application of 2-Azabicyclo[2.2.1]Hept-5-En-3-One (Vince Lactam) in Synthetic Organic and Medicinal Chemistry.

2-Azabicyclo[2.2.1]hept-5-en-3-one (Vince lactam) is known to be a valuable building block in synthetic organic chemistry and drug research. It is an important precursor to access of some blockbuster antiviral drugs such as Carbovir or Abacavir as well as other carbocyclic neuraminidase inhibitors as antiviral agents. The ring C=C bond of the Vince lactam allows versatile chemical manipulations to create not only functionalized γ-lactams, but also γ-amino acid derivatives with a cyclopentane framework. The aim of the current account is to summarize the chemistry of Vince lactam, its synthetic utility and application in organic and medicinal chemistry over the last decade.

Chalcogen Bonding in Selective Recognition and Liquid-Liquid Extraction of Perrhenate.

Efficient recognition and extraction of hazardous anionic pollutants from water medium is of great significance for environmental concerns, representing a challenging area of research in supramolecular chemistry. In this study, we present, for the first time, a comprehensive demonstration of the ability of chalcogen bonding (ChB) to recognize and remove the ReO4 - from 100 % water medium. The anion recognition ability is well elucidated through solution phase NMR and ITC studies, which clearly reveal the selective binding of ReO4 - over other oxo-anions. Moreover, the selenoimidazolium scaffold effectively engages in Se•••O ChB interaction with ReO4 - as confirmed by X-ray crystal structure and XPS analysis. More importantly, the binding of ReO4 - with different prolongations of the σ-holes, along with Se•••Se chalcogen bonding interactions, lead to the formation of a 1D supramolecular assembly. Eventually, ChB receptor Se4Me-Br exhibits ~62 % ReO4 - extraction efficiency through precipitation as the extraction method. Furthermore, in efforts to enhance efficiency, a hydrophobic ChB receptor Se4Do-PF6 has been prepared, achieving an efficiency of up to ~93 % at a very low concentration (~5 ppm) by liquid-liquid extraction.

An acoustofluidic picoinjector

Droplet microfluidics has emerged as a valuable technology for a multitude of chemical and biomedical applications, offering the capability to create independent microenvironments for high-throughput assays. Central to numerous droplet microfluidic applications is the picoinjection of materials into individual droplets, yet existing picoinjection methods often exhibit high power requirements, lack biocompatibility, and/or suffer from limited controllability. Here, we present an acoustofluidic picoinjector that generates acoustic pressure at the droplet interface to enable on-demand, energy-efficient, and biocompatible injection at high precision. We validate our platform by performing acid-base titrations by iteratively injecting picoliter volume reagents into droplets to induce pH transitions detectable by color change in solution. Additionally, we demonstrate the versatility of the acoustofluidic picoinjector in the synthesis of metallic nanoparticles, yielding highly monodisperse and reproducible particle morphologies compared to conventional bulk-phase techniques. By facilitating controlled delivery of reagents or biological samples with unparalleled accuracy, acoustofluidic picoinjection broadens the utility of droplet microfluidics for a myriad of applications in chemical and biological research.

Radiation Chemistry and Radiation Research: A History from the Beginning to the Platinum Edition.

At the dawn of the 20th Century, the underlying chemistry that produced the observed effects of ionizing radiation, e.g., X rays and Radium salts, on aqueous solutions was either unknown or restricted to products found postirradiation. For example, the Curies noted that sealed aqueous solutions of Radium inexplicably decomposed over time, even when kept in the dark. By 1928 there were numerous papers describing the phenomenological effects of ionizing radiation on a wide variety of materials, including the irradiated hands of early radiologists. One scientist who became intensely interested in these radiation effects was Hugo Fricke (Fricke Dosimetry) who established a laboratory in 1928 dedicated to studies on chemical effects of radiation, the results of which he believed were necessary to understand observed radiobiological effects. In this Platinum Issue of Radiation Research (70 years of continuous publication), we present the early history of the development of radiation chemistry and its contributions to all levels of mechanistic radiobiology. We summarize its development as one of the four disciplinary pillars of the Radiation Research Society and its Journal, Radiation Research, founded during the period 1952-1954. In addition, the work of scientists who contributed substantially to the discipline of Radiation Chemistry and to the birth, life and culture of the Society and its journal is presented. In the years following 1954, the increasing knowledge about the underlying temporal and spatial properties of the species produced by various types of radiation is summarized and related to its radiobiology and to modern technologies (e.g., pulsed radiolysis, electron paramagnetic resonance) which became available as the discipline of radiation chemistry developed. A summary of important results from these studies on Radiation Chemistry/Biochemistry in the 20th and 21st Century up to the present time is presented. Finally, we look into the future to see what possible directions radiation chemistry studies might take, based upon promising current research. We find at least two possible directions that will need radiation chemistry expertise to ensure proper experimental design and interpretation of data. These are FLASH radiotherapy, and mechanisms underlying the effects of low doses of radiation delivered at low dose rates. Examples of how radiation chemists could provide beneficial input to these studies are provided.