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Structure Elucidation

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Structure elucidation is the process of determining the molecular structure of a compound using various analytical techniques, such as spectroscopy, chromatography, and crystallography. This process is essential in fields like chemistry and biochemistry for understanding the composition and properties of substances.
lightbulbAbout this topic
Structure elucidation is the process of determining the molecular structure of a compound using various analytical techniques, such as spectroscopy, chromatography, and crystallography. This process is essential in fields like chemistry and biochemistry for understanding the composition and properties of substances.

Key research themes

1. How can hierarchical domain partitioning enhance protein structure elucidation beyond traditional secondary and tertiary annotations?

This research area investigates methods to decompose protein 3D structures into hierarchically organized structural units, such as subdomains and protein units (PUs), complementing classical domain and secondary structure definitions. Understanding proteins at multiple hierarchical levels is crucial for characterizing folding, functionality, and evolution, providing richer insights than single-level annotations.

Key finding: Introduced SWORD2, an integrative web server combining Protein Peeling and domain delineation algorithms to hierarchically decompose proteins into Protein Units (PUs), subdomains, and domains. The method generates multiple... Read more
Key finding: Developed a coarse-grained geometric protein backbone model using only Cα atom positions to describe secondary structures through successive screw motions linking Frenet frames. Validated thresholds for screw parameters... Read more
Key finding: Introduced atomium, a modern Python library that parses multiple macromolecular structure file formats (PDB, mmCIF, MMTF) into a unified data model supporting hierarchical objects such as atoms, residues, chains, and models.... Read more
Key finding: Proposed a sensitivity analysis method of crystal lattice energy to atomic positional variations to assess crystal structure quality. While focused on crystalline small molecules, the methodological emphasis on rigorous... Read more

2. How can advanced computational methods improve the reliability of molecular structure elucidation from spectral data?

This theme examines computational strategies and expert systems that leverage spectroscopic data (notably 1D and 2D NMR, MS, IR) to automate or assist in elucidating molecular structures. Emphasis is on methods addressing complex molecules, integrating diverse spectral inputs, and reducing human error or time expenditure while improving confidence in the identified structures.

Key finding: Chronicled the development of ACD/Structure Elucidator (ACD/SE), an expert system that utilizes extensive NMR data (1D and 2D) to generate candidate molecular structures via fragment assembly, spectral prediction, and... Read more
Key finding: Improved the WebCocon CASE system by incorporating 4J-HMBC (four-bond heteronuclear multiple bond correlation) and NOE (nuclear Overhauser effect) data, extending the HMBC interpretation beyond conventional 2-3 bond... Read more
Key finding: Enhanced the DP4 statistical method by optimizing DFT calculation conditions and updating error distributions to reduce structural uncertainty twofold and improve statistical confidence sevenfold in stereochemical... Read more
Key finding: Provided a comprehensive overview and practical guidance on CASE, focusing on ACD/SE, demonstrating strategies to deduce molecular structures from incomplete, fuzzy, or contradictory spectral data by formulating the inference... Read more

3. What roles do molecular representations and computational analysis of structural parameters play in refining macromolecular and small molecule crystal structures?

This theme addresses computational tools and models for interpreting, validating, and refining structural data of macromolecules and small molecules from crystallographic or spectroscopic experiments. It includes coarse-grained geometric models, software parsers, crystallographic quality assessments, and computational approaches to exploit structural data for improved understanding and prediction of molecular architecture.

Key finding: Reviewed challenges in crystallographic model building and refinement from diffraction data. Emphasized iterative manual inspection alongside automated validation metrics (R-factors, electron density fit, stereochemistry).... Read more
Key finding: Presented an experimentally resolved crystal structure of a novel pyrrole derivative including crystallographic parameters and detailed molecular conformation. Data adds to the structural repository useful for validating... Read more
Key finding: Discussed theoretical and applied advances in shell-like structural mechanics across fields including civil engineering, biomechanics, and materials science. Though not molecular, the mathematical and modeling methodologies... Read more
Key finding: Resolved the structure of a binuclear organotin complex including coordination geometries and supramolecular packing. Demonstrates the necessity of precise crystallographic characterization for understanding metal-ligand... Read more

All papers in Structure Elucidation

Macrocyclic complexes of Cu ( II ), Ni ( II ), Co ( II ), and Zn ( II ) of a tetradentate Schiff base ligand derived from 3benzalideneacetoacetanilide and N -(2aminoethyl )-1,3propanediamine were synthesized . The nature of the complexes... more
An application of the radiolysis method using X-ray synchrotron beam is developed as a novel approach to the synthesis of metal-organic films with controlled shapes and thickness. We demonstrate that a Langmuir monolayer deposited onto a... more
An application of the radiolysis method using X-ray synchrotron beam is developed as a novel approach to the synthesis of metal-organic films with controlled shapes and thickness. We demonstrate that a Langmuir monolayer deposited onto a... more
An application of the radiolysis method using an X-ray synchrotron beam is developed as a novel approach to the synthesis of metal-organic films with controlled shapes and thickness. We demonstrate that a Langmuir monolayer deposited onto... more
HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or... more
A series of 1H-1,2,3-triazole analogs (7a-7d and 9a-9s) were synthesized via "click" chemistry and evaluated for in vitro carbonic anhydrase-II (bovine and human) inhibitory activity. The synthesis of intermediates, 7a and 7c, was... more
A series of 1H-1,2,3-triazole analogs (7a-7d and 9a-9s) were synthesized via "click" chemistry and evaluated for in vitro carbonic anhydrase-II (bovine and human) inhibitory activity. The synthesis of intermediates, 7a and 7c, was... more
A series of 1H-1,2,3-triazole analogs (7a-7d and 9a-9s) were synthesized via "click" chemistry and evaluated for in vitro carbonic anhydrase-II (bovine and human) inhibitory activity. The synthesis of intermediates, 7a and 7c, was... more
A series of 1H-1,2,3-triazole analogs (7a-7d and 9a-9s) were synthesized via "click" chemistry and evaluated for in vitro carbonic anhydrase-II (bovine and human) inhibitory activity. The synthesis of intermediates, 7a and 7c, was... more
A bicyclic unsaturated 1,2-diol framework was found to undergo an interesting set of domino reactions on treatment with oxidants. One-pot syntheses of seven-membered-ringcontaining frameworks were achieved by a Pb(OAc) 4 -mediated domino... more
A bicyclic unsaturated 1,2-diol framework was found to undergo an interesting set of domino reactions on treatment with oxidants. One-pot syntheses of seven-membered-ringcontaining frameworks were achieved by a Pb(OAc) 4 -mediated domino... more
The aroma composition of autoxidized arachidonic acid was characterized by aroma extract dilution analysis. The most potent odorant was trans-4,5-epoxy-(E)-2-decenal followed by 1-octen-3-one, (E,Z)-2,4-decadienal,... more
Centaurea asutro-anatolica Hub.-Mor. and C. kizildaghensis Uzunh., E. Doğan & H. Duman, two indigenous perennial herbs from the Turkish flora, belong to the medicinally important genus Centaurea L. (fam: Asteraceae), which comprises ca.... more
Centaurea asutro-anatolica Hub.-Mor. and C. kizildaghensis Uzunh., E. Doğan & H. Duman, two indigenous perennial herbs from the Turkish flora, belong to the medicinally important genus Centaurea L. (fam: Asteraceae), which comprises ca.... more
3D molecular structure determination is a challenge for organic compounds or natural products available in minute amounts. Proton/proton and proton/carbon correlations yield the constitution. J couplings and NOEs oftentimes supported by... more
Irradiation of a substituted ansa-titanocene(IV) dihydroxido complex with visible light induces Ti-O bond dissociation. In contrast to previous studies on structurally similar unbridged complexes, no side reactions are observed and... more
Anthocephalusine A (1) and 3β‐isodihydrocadambine 4‐oxide (2) were isolated from the leaves of Anthocephalus chinensis (Rubiaceae), together with five known compounds. The structures were established by spectroscopic methods including... more
p-Cholorosulfinylaniline was prepared by the reaction of p-chloroaniline and SOCl2. The structural, conformational and configurational properties of the obtained liquid compound were studied by Raman and infrared spectroscopy in the... more
The enzyme type 5 17β-hydroxysteroid dehydrogenase 5 (17β-HSD5) catalyzes the transformation of androstenedione (4-dione) to testosterone (T) in the prostate. This metabolic pathway remains active in cancer patients receiving androgen... more
The tetrapyrrolic chlorophyllc atabolites (or phyllobilins, PBs) were analyzed in yellow fall leaveso ft he grape Chardonnay,acommon Vitis vinifera white wine cultivar.T he major fractionsi nl eaf extractso fV. vinifera,t entatively... more
Synthesis of a series of the substituted [(pyridinyl and pyrimidin-2-ylimino)-ethyl]-4hydroxy-chromen-2-ones and their tetrazole derivates is presented in this study. By catalytic condensation of 4-hydroxy-3-acetylcoumarine 2 and... more
Sea cucumbers produce numerous compounds with a wide range of chemical structural diversity. Among these, saponins are the most diverse and include sulfated, non-sulfated, acetylated and methylated congeners with different aglycone and... more
Background The escalating global challenge of antibiotic resistance severely restricts our ability to treat common infectious diseases, necessitating the urgent need for the development of novel antibiotics with distinct mechanisms of... more
Tetraamminecopper perchlorate (TACP) is one of the most interesting explosive copper perchlorate-ammonia complexes. Despite the fact that this complex has been known for more than 100 years there is very little information in the... more
The palatability of various organs (body wall, cuvierian gland, viscera, longitudinal muscle bands and gonads) of sea cucumber Holothuria leucospilota (Brandt) was studied by feeding experiments, performed on a freshwater fish... more
Forced degradation studies are an essential component of pharmaceutical development, designed to intentionally degrade drug substances and products under conditions more rigorous than standard accelerated conditions. These studies play a... more
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