Structural Assignment Research Articles

Teaching Students to Think Creatively (in Drawing Classes)

In the first way of developing spatial imagination, the spatial imagination of students is increased by using drawings given on objects, mentally dividing them into simple figures and drawing up their clear image. Indeed, if there is a clear image of the object depicted in the figure, it becomes easier for the student to visualize the object, the appearance of which is given in the figures. Through a qualitative analysis of teaching methodologies and student experiences, this research investigates the strategies employed by art instructors to stimulate creative thinking in drawing classes. It explores how instructors design curriculum, structure assignments, and provide feedback to encourage students to approach drawing with imagination and inventiveness. Furthermore, this study examines the impact of these teaching practices on students' creative development and artistic growth. By analyzing student artworks, reflections, and assessments, it evaluates the effectiveness of different pedagogical approaches in nurturing creative thinking skills. The findings of this research shed light on the importance of teaching students to think creatively in drawing classes and offer practical insights for art educators seeking to enhance their teaching practices. By fostering a supportive and stimulating learning environment that encourages experimentation and risk-taking, instructors can empower students to unlock their creative potential and develop as artists. This research contributes to our understanding of the role of creativity in art education and provides valuable guidance for educators striving to cultivate creative thinking skills in their students within the context of drawing classes.

Chromatograms and Mass Spectra of High-Mannose and Paucimannose N-Glycans for Rapid Isomeric Identifications.

N-Linked glycosylation is one of the most essential post-translational modifications of proteins. However, N-glycan structural determination remains challenging because of the small differences in structures between isomers. In this study, we constructed a database containing collision-induced dissociation MSn mass spectra and chromatograms of high-performance liquid chromatography for the rapid identification of high-mannose and paucimannose N-glycan isomers. These N-glycans include isomers by breaking of arbitrary numbers of glycosidic bonds at arbitrary positions of canonical Man9GlcNAc2 N-glycans. In addition, some GlcMannGlcNAc2 N-glycan isomers were included in the database. This database is particularly useful for the identification of the N-glycans not in conventional N-glycan standards. This study demonstrated the application of the database to structural assignment for high-mannose N-glycans extracted from bovine whey proteins, soybean proteins, human mammary epithelial cells, and human breast carcinoma cells. We found many N-glycans that are not expected to be generated by conventional biosynthetic pathways of multicellular eukaryotes.

A Very Deep Graph Convolutional Network for 13C NMR Chemical Shift Calculations with Density Functional Theory Level Performance for Structure Assignment.

Nuclear magnetic resonance (NMR) chemical shift calculations are powerful tools for structure elucidation and have been extensively employed in both natural product and synthetic chemistry. However, density functional theory (DFT) NMR chemical shift calculations are usually time-consuming, while fast data-driven methods often lack reliability, making it challenging to apply them to computationally intensive tasks with a high requirement on quality. Herein, we have constructed a 54-layer-deep graph convolutional network for 13C NMR chemical shift calculations, which achieved high accuracy with low time-cost and performed competitively with DFT NMR chemical shift calculations on structure assignment benchmarks. Our model utilizes a semiempirical method, GFN2-xTB, and is compatible with a broad variety of organic systems, including those composed of hundreds of atoms or elements ranging from H to Rn. We used this model to resolve the controversial J/K ring junction problem of maitotoxin, which is the largest whole molecule assigned by NMR calculations to date. This model has been developed into user-friendly software, providing a useful tool for routine rapid structure validation and assignation as well as a new approach to elucidate the large structures that were previously unsuitable for NMR calculations.

Assignment of individual structures from intermetalloid nickel gallium cluster ensembles

Poorly selective mixed-metal cluster synthesis and separation yield reaction solutions of inseparable intermetalloid cluster mixtures, which are often discarded. High-resolution mass spectrometry, however, can provide precise compositional data of such product mixtures. Structure assignments can be achieved by advanced computational screening and consideration of the complete structural space. Here, we experimentally verify structure and composition of a whole cluster ensemble by combining a set of spectroscopic techniques. Our study case are the very similar nickel/gallium clusters of M12, M13 and M14 core composition Ni6+xGa6+y (x + y ≤ 2). The rationalization of structure, bonding and reactivity is built upon the organometallic superatom cluster [Ni6Ga6](Cp*)6 = [Ga6](NiCp*)6 (1; Cp* = C5Me5). The structural conclusions are validated by reactivity tests using carbon monoxide, which selectively binds to Ni sites, whereas (triisopropylsilyl)acetylene selectively binds to Ga sites.

Structural Assignment of the Product Ion Generated from a Natural Ciguatoxin-3C Congener, 51-Hydroxyciguatoxin-3C, and Discovery of Distinguishable Signals in Congeners Bearing the 51-Hydroxy Group.

Ciguatoxins (CTXs) stand as the primary toxins causing ciguatera fish poisoning (CFP) and are essential compounds distinguished by their characteristic polycyclic ether structure. In a previous report, we identified the structures of product ions generated via homolytic fragmentation by assuming three charge sites in the mass spectrometry (MS)/MS spectrum of ciguatoxin-3C (CTX3C) using LC-MS. This study aims to elucidate the homolytic fragmentation of a ciguatoxin-3C congener. We assigned detailed structures of the product ions in the MS/MS spectrum of a naturally occurring ciguatoxin-3C congener, 51-hydroxyciguatoxin-3C (51-hydoxyCTX3C), employing liquid chromatography/quadrupole time-of-flight mass spectrometry with an atmospheric pressure chemical ionization (APCI) source. The introduction of a hydroxy substituent on C51 induced different fragmentation pathways, including a novel cleavage mechanism of the M ring involving the elimination of 51-OH and the formation of enol ether. Consequently, new cleavage patterns generated product ions at m/z 979 (C55H79O15), 439 (C24H39O7), 149 (C10H13O), 135 (C9H11O), and 115 (C6H11O2). Additionally, characteristic product ions were observed at m/z 509 (C28H45O8), 491 (C28H43O7), 481 (C26H41O8), 463 (C26H39O7), 439 (C24H39O7), 421 (C24H37O6), 171 (C9H15O3), 153 (C9H13O2), 141 (C8H13O2), and 123 (C8H11O).

해외 음악이론 소프트웨어를 활용한 수업 사례: 대학 화성학 강좌를 위한 ‘뮤지션’(Musition) 프로그램

This paper aims to present a case study on the utilization of the music theory software 'Musition' in harmony courses. Thus, this paper first examines the evolution of music theory education abroad, exploring specific applications in university-level harmony courses. 'Musition,' developed by the Australian company Rising Software, is a music theory software that spans fundamental music theory to advanced harmonies and four-part writings, providing a tremendous number of syllabi, contents, assignments, and exams, which are applicable to university music theory curricula.
 Through the use of 'Musition,' several key advantages have been identified. Instructors can plan their classes freely according to the course content and structure assignments and exams using a substantial number of examples and contents. Furthermore, automatic generation of grading and student evaluation reports are available, even in complex four-part writings. Considering the key features of Musition, this papers argues that the development of music theory software not only eases the burden on instructors in lesson planning, grading, and student management but also encourages students' self-directed learning. I hope such music theory software will be applicable to music theory education in Korea.

해외 음악이론 소프트웨어를 활용한 수업 사례: 대학 화성학 강좌를 위한 ‘뮤지션’(Musition) 프로그램

This paper aims to present a case study on the utilization of the music theory software 'Musition' in harmony courses. Thus, this paper first examines the evolution of music theory education abroad, exploring specific applications in university-level harmony courses. 'Musition,' developed by the Australian company Rising Software, is a music theory software that spans fundamental music theory to advanced harmonies and four-part writings, providing a tremendous number of syllabi, contents, assignments, and exams, which are applicable to university music theory curricula.
 Through the use of 'Musition,' several key advantages have been identified. Instructors can plan their classes freely according to the course content and structure assignments and exams using a substantial number of examples and contents. Furthermore, automatic generation of grading and student evaluation reports are available, even in complex four-part writings. Considering the key features of Musition, this papers argues that the development of music theory software not only eases the burden on instructors in lesson planning, grading, and student management but also encourages students' self-directed learning. I hope such music theory software will be applicable to music theory education in Korea.

Comparative Analysis of Site-Specific N-glycosylation of LAMP1 from Breast Cancer Tissues.

Glycosylation changes in cancer proteins have been associated with malignant transformation. However, techniques for analyzing site-specific glycosylation changes in target proteins obtained from clinical tissue samples are insufficient. To overcome these problems, we developed a targeted N-glycoproteomic approach consisting of immunoprecipitation, glycopeptide enrichment, LC/MS/MS and structural assignment using commercially available analytical software followed by manual confirmation. This approach was applied to the comparative site-specific glycosylation analysis of lysosome-associated membrane glycoprotein 1 (LAMP1) between breast cancer (BC) tumors and normal tissues adjacent to tumors. Extensive determination of glycan heterogeneity from four N-glycosylation sites (Asn84/103/249/261) in LAMP1 identified 262 glycoforms and revealed remarkable diversity in tumor glycan structures. A significant increase in N-glycoforms with multiple fucoses and sialic acids at Asn84/249 and high-mannose-type glycans at Asn103/261 were observed in the tumor. Principal component analysis revealed that tumors of different subtypes have independent distributions. This approach enables site-specific glycopeptide analysis of target glycoprotein in breast cancer tissue and become a powerful tool for characterizing tumors with different pathological features by their glycan profiles.

Polyketides from Neohelicosporium griseum: structure assignment and bioactivity investigation

Polyketides from Neohelicosporium griseum: structure assignment and bioactivity investigation

New N-Adducts of Thiadiazole and Thiazoline with Levoglucosenone and Evaluation of Their Significant Cytotoxic (Anti-Cancer) Activity.

The conjugate N-adducts of thio-1,3,4-diazole and 2-thiazoline with levoglucosenone were synthesized via a stereoselective, base-catalyzed conjugate N-Michael addition to levoglucosenone at C-4. Structural assignments were established using 1H and 13C NMR analysis, and X-ray single-crystal analysis for one of the compounds. The biological properties of the novel compounds were tested on a cell model. Cytotoxicity was analyzed via colorimetric assay. Two distinct types of cell death, apoptosis and necrosis, were analyzed by determining the phosphatidylserine levels from the outer leaflet of the plasma membrane, caspase activation, and lactate dehydrogenase release. We also evaluated DNA damage using an alkaline comet assay. The level of oxidative stress was measured with a modified comet assay and an H2DCFDA probe. The thio-1,3,4-diazole adduct (FCP23) and the 2-thiazoline adduct (FCP26) exhibit similar cytotoxicity values for cancer cells (ovarian (A2780), breast (MCF-7), cervix (HeLa), colon (LoVo), and brain (MO59J and MO59K)), but their mechanism of action is drastically different. While FCP23 induces oxidative stress, DNA damage, and necrosis, FCP26 induces apoptosis through caspase activation.

Incorporating Journal Articles in a Game Theory Course Using Structured Assignments

Incorporating Journal Articles in a Game Theory Course Using Structured Assignments

A screening method for the quantitative determination of selective androgen receptor modulators (SARMs) in capsules by high resolution 19F- and 1H-NMR spectroscopy.

A new method for rapid determination of the content of selective androgenic receptor modulators (SARMs) andarine, cardarine, ligandrol, ostarine and S-23 in capsules by 1H- and 19F-high resolution nuclear magnetic resonance spectroscopy was described and validated. Specificity, linearity, accuracy, precision, detection and quantification limits were considered as validation parameters. Full 1H-, 13C- and 19F-NMR structural assignment of the SARMs is provided as a tool for self-standing identification without a reference standard. Amounts of 7-15 mg of SARMs/capsule were detected in different products with an intermediate precision of 0.8-1.7% in 4 to 20 minutes of analysis time. The validation results and rapidity of analysis confirm the applicability of the method for large-scale screening. The statistical analysis of the results from 19F- and 1H-quantitative NMR showed that both approaches were equally effective, thus expanding the potential use of the methodology to non-fluorinated SARMs. At present, no SARM has been approved for human consumption; however, SARMs are actually used by bodybuilders and recreational athletes, who purchase them even though the risk-benefit ratio of these molecules has not been definitively established.

Revisiting Biginelli-like reactions: solvent effects, mechanisms, biological applications and correction of several literature reports.

This study critically reevaluates reported Biginelli-like reactions using a Kamlet-Abboud-Taft-based solvent effect model. Surprisingly, structural misassignments were discovered in certain multicomponent reactions, leading to the identification of pseudo three-component derivatives instead of the expected MCR adducts. Attempts to replicate literature conditions failed, prompting reconsideration of the described MCRs and proposed mechanisms. Electrospray ionization (tandem) mass spectrometry, NMR, melting points, elemental analyses and single-crystal X-ray analysis exposed inaccuracies in reported MCRs and allowed for the proposition of a complete catalytic cycle. Biological investigations using both pure and "contaminated" derivatives revealed distinctive features in assessed bioassays. A new cellular action mechanism was unveiled for a one obtained pseudo three-component adduct, suggesting similarity with the known dihydropyrimidinone Monastrol as Eg5 inhibitors, disrupting mitosis by forming monoastral mitotic spindles. Docking studies and RMSD analyses supported this hypothesis. The findings described herein underscore the necessity for a critical reexamination and potential corrections of structural assignments in several reports. This work emphasizes the significance of rigorous characterization and critical evaluation in synthetic chemistry, urging a careful reassessment of reported synthesis and biological activities associated with these compounds.

DFT-based 11B solid-state NMR calculations for guiding fine local structure identification and phase-property modulation in ZnxY1-xBO3-0.5x borate oxide ion conductors.

Solid-state nuclear magnetic resonance (NMR) spectroscopy serves as a powerful technique for probing local structures. However, the interpretation of NMR signals mainly based on empirical knowledge could lead to imprecise local structural determinations. To address this, density functional theory (DFT)-based theoretical NMR calculations, aided by experimental three-dimensional continuous rotation electronic diffraction (3D cRED) technique, were performed for ZnxY1-xBO3-0.5x borate oxide ion conductors. The calculations provided fine local structure identification for the experimental 11B NMR spectra of ZnxY1-xBO3-0.5x, providing rich information on multiple experimental 11B NMR signals towards the complex boron oxide anions associated with bridging oxygen vacancies and the coexistence of the monoclinic (C2/c), hexagonal (P63/m), and trigonal (R32) phases in ZnxY1-xBO3-0.5x. Owing to the advantages of solid-state NMR in identifying closely related phases compared to X-ray/neutron diffraction technique, along with the advanced 3D cRED technique that allows for rapid phase identification and structure determination, we provide a fine local structure identification and a more inclusive insight into the coexistence of multiple phases in borate with the same composition. More importantly, this work provides guidance for phase and property modulation. Phase modulation in ZnxY1-xBO3-0.5x was carried out with thermodynamic and kinetic modulation and eventually realized the tuning of the local structures and the resultant oxide ion conductivity of ZnxY1-xBO3-0.5x. This work provides a theoretical and experimental platform to access the flexible structural assignment of boron oxide anions and therefore offers new guidance and insights into the defect structures and the phase-property modulation of inorganic solid functional materials beyond borate oxide ion conductors.

Impacts of basis sets, solvent models, and NMR methods on the accuracy of 1H and 13C chemical shift calculations for biaryls: a DFT study

Introduction: Biaryls are core structures composed of chiral ligands, organocatalysts, biologically active natural products and biopolymer lignins. In this study, the effects of basis sets, solvent models, and NMR methods on the accuracy of 1H/13C NMR chemical shift calculations for biaryl structures were evaluated. Methods: All calculations were performed using Gaussian09. The GIAO NMR results were observed and extracted using GaussView05. To reduce the systematic error of the calculations, linear regression analysis of the calculated chemical shifts versus the experimental shifts was performed. Results: The tested basis sets showed good 1H/13C results, with CMAE values as low as 0.0425 ppm and 1.09 ppm for 1H and 13C, respectively. The use of solvent models significantly increased the accuracy of the 1H chemical shift calculations. The GIAO method produced more accurate results than did the IGAIM and CSGT methods. Conclusion: This study recommends 6-31G(d,p) and DGDZVP basis sets, IEMPCM and CPCM solvent models, and GIAO NMR methods for the accurate prediction of 1H and 13C chemical shifts for biaryls, assisting in their full structural assignments.

Structural and functional analysis of engineered antibodies for cancer immunotherapy: insights into protein compactness and solvent accessibility

Antibodies are crucial tools in various biomedical applications, including immunotherapy. In this study, we focused on designing and engineering antibodies to enhance their structural dynamics and functional properties. By employing advanced computational techniques and experimental validation, we gained crucial insights into the impact of specific mutations on the engineered antibodies. This study investigates the design and engineering of antibodies to improve their structural dynamics and functional properties. Structural attributes, such as protein compactness and solvent accessibility, were assessed, revealing interesting trends in anti-CD3 and anti-HER2 antibodies. Mutations in CD3 antibodies resulted in a more stable conformation, while mutant HER2 antibodies exhibited altered interaction with the target. Analysis of secondary structure assignments demonstrated significant changes in the folding and stability of the mutant antibodies compared to the wild-type counterparts. The conformational landscape of the engineered antibodies was explored, providing insights into folding pathways and binding mechanisms. Overall, the current study highlights the significance of antibody design and engineering in modulating structural dynamics and functional properties. The findings contribute to developing improved immunotherapeutic strategies by optimising antibody-based therapeutics for targeted diseases with enhanced efficacy and precision. Communicated by Ramaswamy H. Sarma

Synthesis, Characterizations, and Quantum Chemical Investigations on Imidazo[1,2-a]pyrimidine-Schiff Base Derivative: (E)-2-Phenyl-N-(thiophen-2-ylmethylene)imidazo[1,2-a]pyrimidin-3-amine.

In this study, (E)-2-phenyl-N-(thiophen-2-ylmethylene)imidazo[1,2-a]pyrimidin-3-amine (3) is synthesized, and detailed spectral characterizations using 1H NMR, 13C NMR, mass, and Fourier transform infrared (FT-IR) spectroscopy were performed. The optimized geometry was computed using the density functional theory method at the B3LYP/6-311++G(d,p) basis set. The theoretical FT-IR and NMR (1H and 13C) analysis are agreed to validate the structural assignment made for (3). Frontier molecular orbitals, molecular electrostatic potential, Mulliken atomic charge, electron localization function, localized orbital locator, natural bond orbital, nonlinear optical, Fukui functions, and quantum theory of atoms in molecules analyses are undertaken and meticulously interpreted, providing profound insights into the molecular nature and behaviors. In addition, ADMET and drug-likeness studies were carried out and investigated. Furthermore, molecular docking and molecular dynamics simulations have been studied, indicating that this is an ideal molecule to develop as a potential vascular endothelial growth factor receptor-2 inhibitor.

106-fold faster C-H bond hydroxylation by a CoIII,IV2(µ-O)2 complex [via a CoIII2(µ-O)(µ-OH) intermediate] versus its FeIIIFeIV analog.

The hydroxylation of C-H bonds can be carried out by the high-valent CoIII,IV2(µ-O)2 complex 2a supported by the tetradentate tris(2-pyridylmethyl)amine ligand via a CoIII2(µ-O)(µ-OH) intermediate (3a). Complex 3a can be independently generated either by H-atom transfer (HAT) in the reaction of 2a with phenols as the H-atom donor or protonation of its conjugate base, the CoIII2(µ-O)2 complex 1a. Resonance Raman spectra of these three complexes reveal oxygen-isotope-sensitive vibrations at 560 to 590 cm-1 associated with the symmetric Co-O-Co stretching mode of the Co2O2 diamond core. Together with a Co•••Co distance of 2.78(2) Å previously identified for 1a and 2a by Extended X-ray Absorption Fine Structure (EXAFS) analysis, these results provide solid evidence for their "diamond core" structural assignments. The independent generation of 3a allows us to investigate HAT reactions of 2a with phenols in detail, measure the redox potential and pKa of the system, and calculate the O-H bond strength (DO-H) of 3a to shed light on the C-H bond activation reactivity of 2a. Complex 3a is found to be able to transfer its hydroxyl ligand onto the trityl radical to form the hydroxylated product, representing a direct experimental observation of such a reaction by a dinuclear cobalt complex. Surprisingly, reactivity comparisons reveal 2a to be 106-fold more reactive in oxidizing hydrocarbon C-H bonds than corresponding FeIII,IV2(µ-O)2 and MnIII,IV2(µ-O)2 analogs, an unexpected outcome that raises the prospects for using CoIII,IV2(µ-O)2 species to oxidize alkane C-H bonds.

Spectroscopic, quantum computational, topological, Fukui functions and molecular docking analysis on a potential anti-cancer molecule Nicotinamide by DFT method

Nicotinamide has been identified as an anti-oxidant, anti-inflammatory and anti-tumorigenic activity in the medical field. To evaluate the cytotoxic effects of nicotinamide against cancer cells; a detailed spectroscopic investigation was made and examined through FT-IR, FT-Raman and UV–Vis techniques. For quantum computational calculation, the DFT method was performed in order to identify the structural and vibrational assignments of the molecule on the basis of the potential energy distribution. The Time-dependent DFT method was applied to compute electronic excitation and predict UV–Vis spectra. The molecular electrostatic potential, frontier molecular orbitals, natural bond orbital, electronic localization function and localized orbital locator were analyzed to study the topological, chemical reactivity and bioactivity nature of the molecule by suitable computational techniques. The scatter plot of the reduced density gradients was constructed to predict the weak interactions. In addition to these analyses, the local reactivity descriptors like the local softness and Fukui functions were obtained. Furthermore, the molecular docking studies of the molecule were carried out to analyze the biological activity against cancer cells with the target proteins under the class of Poly (adenosine diphosphate-ribose) polymerase enzyme inhibitors and the respective docking parameters were calculated. As per the investigation, the anti-cancer activity had revealed based on molecular docking analysis and it had been identified that the nicotinamide molecule could act as a good inhibitor against cancer.

1,6-Dioxo-2-azaspiro[3.4]oct-2-enes and Related Spirocycles: Heterocycles from [3 + 2] Nitrile Oxide Cycloadditions with 2-Methyleneoxetanes, -Thietanes, and -Azetidines.

Isoxazolines and 4-membered heterocycles are significant structural motifs in numerous synthetic intermediates and natural products. [3 + 2] Cycloadditions between enol ethers and nitrile oxides have been well studied; however, nitrile oxide cycloadditions with 4-membered heterocycles to give spiroisoxazolines are unreported. Here, we showcase the regio- and diastereoselective [3 + 2] nitrile oxide cycloadditions of 2-methyleneoxetanes, -azetidines, and -thietanes to give an array of 1,6-dioxo-2-azaspiro[3.4]oct-2-enes and related spirocycles. 2D NMR experiments suggested that most of the observed diastereoselectivities were dictated by steric interactions; however, dipolarophiles with H bonding donors reversed the stereochemical outcome. X-ray crystallography confirmed the structural assignments.