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primaryClass={cs.FL},
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url={https://arxiv.org/abs/1603.02481},
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}
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@inproceedings{networkx,
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abstract = {NetworkX is a Python language package for exploration
|
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and analysis of networks and network algorithms.
|
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The core package provides data structures
|
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for representing many types of networks, or graphs,
|
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including simple graphs, directed graphs, and graphs
|
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with parallel edges and self-loops. The nodes in NetworkX
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graphs can be any (hashable) Python object
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and edges can contain arbitrary data; this flexibility
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makes NetworkX ideal for representing networks
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found in many different scientific fields.
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In addition to the basic data structures many graph
|
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algorithms are implemented for calculating network
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properties and structure measures: shortest paths,
|
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betweenness centrality, clustering, and degree distribution
|
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and many more. NetworkX can read and
|
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write various graph formats for easy exchange with
|
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existing data, and provides generators for many
|
||||
classic graphs and popular graph models, such as
|
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the Erdos-Renyi, Small World, and Barabasi-Albert
|
||||
models.
|
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The ease-of-use and flexibility of the Python programming
|
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language together with connection to the
|
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SciPy tools make NetworkX a powerful tool for scientific
|
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computations. We discuss some of our recent
|
||||
work studying synchronization of coupled oscillators
|
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to demonstrate how NetworkX enables research in
|
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the field of computational networks.},
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added-at = {2008-09-24T13:11:32.000+0200},
|
||||
address = {Pasadena, CA USA},
|
||||
author = {Hagberg, Aric A. and Schult, Daniel A. and Swart, Pieter J.},
|
||||
biburl = {https://www.bibsonomy.org/bibtex/272096c6553d7057409fe78ca698eb332/mschuber},
|
||||
booktitle = {Proceedings of the 7th Python in Science Conference},
|
||||
editor = {Varoquaux, Ga\"el and Vaught, Travis and Millman, Jarrod},
|
||||
interhash = {7a78aca0e0e5adfc4d7e882e4635435f},
|
||||
intrahash = {72096c6553d7057409fe78ca698eb332},
|
||||
keywords = {2008 analysis network python tool},
|
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pages = {11 - 15},
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||||
timestamp = {2008-09-24T13:11:32.000+0200},
|
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title = {Exploring Network Structure, Dynamics, and Function using NetworkX},
|
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url = {http://conference.scipy.org/proceedings/SciPy2008/paper_2/},
|
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year = 2008
|
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}
|
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@article{rdkit,
|
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added-at = {2017-04-11T06:11:47.000+0200},
|
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author = {Landrum, Greg},
|
||||
biburl = {https://www.bibsonomy.org/bibtex/28d01fceeccd6bf2486e47d7c4207b108/salotz},
|
||||
description = {Release 2016_09_4 (Q3 2016) Release · rdkit/rdkit},
|
||||
interhash = {ee9a4ddeff3121aa622cf35709fa6e21},
|
||||
intrahash = {8d01fceeccd6bf2486e47d7c4207b108},
|
||||
keywords = {chemoinformatics drug-design pharmacophores software},
|
||||
timestamp = {2017-04-11T06:11:47.000+0200},
|
||||
title = {RDKit: Open-Source Cheminformatics Software},
|
||||
url = {https://github.com/rdkit/rdkit/releases/tag/Release_2016_09_4},
|
||||
year = 2016
|
||||
}
|
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@article{avogadro,
|
||||
author={Hanwell, Marcus D.
|
||||
and Curtis, Donald E.
|
||||
and Lonie, David C.
|
||||
and Vandermeersch, Tim
|
||||
and Zurek, Eva
|
||||
and Hutchison, Geoffrey R.},
|
||||
title={Avogadro: an advanced semantic chemical editor, visualization, and analysis platform},
|
||||
journal={Journal of Cheminformatics},
|
||||
year={2012},
|
||||
month={Aug},
|
||||
day={13},
|
||||
volume={4},
|
||||
number={1},
|
||||
pages={17},
|
||||
abstract={The Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible, high quality rendering, and a powerful plugin architecture. Typical uses include building molecular structures, formatting input files, and analyzing output of a wide variety of computational chemistry packages. By using the CML file format as its native document type, Avogadro seeks to enhance the semantic accessibility of chemical data types.},
|
||||
issn={1758-2946},
|
||||
doi={10.1186/1758-2946-4-17},
|
||||
url={https://doi.org/10.1186/1758-2946-4-17}
|
||||
}
|
||||
@article{nmrbin,
|
||||
title = {A novel spectra similarity measure},
|
||||
journal = {Chemometrics and Intelligent Laboratory Systems},
|
||||
volume = {85},
|
||||
number = {1},
|
||||
pages = {1-8},
|
||||
year = {2007},
|
||||
issn = {0169-7439},
|
||||
doi = {https://doi.org/10.1016/j.chemolab.2005.10.002},
|
||||
url = {https://www.sciencedirect.com/science/article/pii/S0169743905001620},
|
||||
author = {Lorant Bodis and Alfred Ross and Ernö Pretsch},
|
||||
keywords = {Spectra comparison, NMR spectra, Quality control},
|
||||
abstract = {A new method is described for calculating the similarity degree of two spectra. Its performance is optimized with similar, computer-generated 1H NMR spectra. The method is compared with a recently proposed local cross-correlation method. Using a test set, its power to discriminate between related and unrelated 1H NMR spectra is better than with the cross-correlation method. Better results are also obtained when comparing measured spectra of a database with the corresponding estimated ones or with estimated spectra of randomly assigned structures. Although, so far, it has only been tested with 1H NMR spectra, due to the generality of the approach, the novel procedure can be applied to comparing other spectra or patterns as well.}
|
||||
}
|
||||
@misc{gurobi,
|
||||
author = {{Gurobi Optimization, LLC}},
|
||||
title = {{Gurobi Optimizer Reference Manual}},
|
||||
year = {2026},
|
||||
url = {https://www.gurobi.com}
|
||||
}
|
||||
@Article{caffeinesynth,
|
||||
AUTHOR = {Lin, Zhipeng and Wei, Jian and Hu, Yongqiang and Pi, Dujuan and Jiang, Mingguo and Lang, Tao},
|
||||
TITLE = {Caffeine Synthesis and Its Mechanism and Application by Microbial Degradation, A Review},
|
||||
JOURNAL = {Foods},
|
||||
VOLUME = {12},
|
||||
YEAR = {2023},
|
||||
NUMBER = {14},
|
||||
ARTICLE-NUMBER = {2721},
|
||||
URL = {https://www.mdpi.com/2304-8158/12/14/2721},
|
||||
PubMedID = {37509813},
|
||||
ISSN = {2304-8158},
|
||||
ABSTRACT = {Caffeine is a metabolite derived from purine nucleotides, typically accounting for 2–5 Percent of the dry weight of tea and 1–2 Percent of the dry weight of coffee. In the tea and coffee plants, the main synthesis pathway of caffeine is a four-step sequence consisting of three methylation reactions and one nucleosidase reaction using xanthine as a precursor. In bacteria, caffeine degradation occurs mainly through the pathways of N-demethylation and C-8 oxidation. However, a study fully and systematically summarizing the metabolism and application of caffeine in microorganisms has not been established elsewhere. In the present study, we provide a review of the biosynthesis, microbial degradation, gene expression, and application of caffeine microbial degradation. The present review aims to further elaborate the mechanism of caffeine metabolism by microorganisms and explore the development prospects in this field.},
|
||||
DOI = {10.3390/foods12142721}
|
||||
}
|
||||
@Article{vanillinesynth,
|
||||
AUTHOR = {Tazon, Arnold William and Awwad, Fatima and Meddeb-Mouelhi, Fatma and Desgagné-Penix, Isabel},
|
||||
TITLE = {Biotechnological Advances in Vanillin Production: From Natural Vanilla to Metabolic Engineering Platforms},
|
||||
JOURNAL = {BioChem},
|
||||
VOLUME = {4},
|
||||
YEAR = {2024},
|
||||
NUMBER = {4},
|
||||
PAGES = {323--349},
|
||||
URL = {https://www.mdpi.com/2673-6411/4/4/17},
|
||||
ISSN = {2673-6411},
|
||||
ABSTRACT = {Vanillin, an aromatic aldehyde, is one of the most popular flavors worldwide, extensively used in the food, cosmetics, pharmaceutical, and agrochemical industries. Despite its widespread use, less than 1 Percent of the total vanillin production is natural, with the majority being synthesized chemically. While chemical synthesis can help to meet the growing demand for vanillin, a strong market trend has rapidly developed for products created from natural ingredients, including natural vanillin. Given the labor-intensive process of extracting vanillin from vanilla pods, there is a critical need for new metabolic engineering platforms to support the biotechnological production of nature-identical vanillin. This review highlights the significance of vanillin in various markets, its diverse applications, and the current state of bio-engineered production using both prokaryotic and eukaryotic biological systems. Although recent advancements have demonstrated successful vanillin production through biocatalytic approaches, our focus was to provide a current and innovative overview of vanillin bioengineering across various host systems with special consideration placed on microalgae, which are emerging as promising platforms for vanillin production through metabolic engineering. The use of these systems to support the biotechnological production of vanillin, while leveraging the photosynthetic capabilities of microalgae to capture CO2 and convert it into biomass, can significantly reduce the overall carbon footprint.},
|
||||
DOI = {10.3390/biochem4040017}
|
||||
}
|
||||
@article{xanthinnmr,
|
||||
author = {Benoit, Robert L. and Fréchette, Monique},
|
||||
title = {Protonation of hypoxanthine, guanine, xanthine, and caffeine},
|
||||
journal = {Canadian Journal of Chemistry},
|
||||
volume = {63},
|
||||
number = {11},
|
||||
pages = {3053-3056},
|
||||
year = {1985},
|
||||
doi = {10.1139/v85-506},
|
||||
URL = {
|
||||
https://doi.org/10.1139/v85-506
|
||||
},
|
||||
eprint = {
|
||||
https://doi.org/10.1139/v85-506
|
||||
}
|
||||
,
|
||||
abstract = { The protonation equilibria of three hydroxypurines, hypoxanthine, guanine, and xanthine, and of related caffeine have been studied by 1H and 13C nmr and uv spectroscopies in aqueous sulfuric or perchloric acids. The results have been interpreted on the basis of the excess acidity method. The values and the protonation sites are discussed and comparisons are made with results of recent theoretical calculations. }
|
||||
}
|
||||
@article{manyxanthinesnmr,
|
||||
author = {Mueller, Christa E. and Shi, Dan and Manning, Malcolm, Jr. and Daly, John W.},
|
||||
title = {Synthesis of paraxanthine analogs (1,7-disubstituted xanthines) and other xanthines unsubstituted at the 3-position: structure-activity relationships at adenosine receptors},
|
||||
journal = {Journal of Medicinal Chemistry},
|
||||
volume = {36},
|
||||
number = {22},
|
||||
pages = {3341-3349},
|
||||
year = {1993},
|
||||
month = {10},
|
||||
issn = {0022-2623},
|
||||
doi = {10.1021/jm00074a015},
|
||||
url = {https://doi.org/10.1021/jm00074a015},
|
||||
eprint = {https://pubs.acs.org/jmcmar/article-pdf/36/22/3341/7236147/jm00074a015.pdf},
|
||||
}
|
||||
@article{7xanthinnmr,
|
||||
author = {Jayantha, Bhagya and Zhang, Shuyuan and Summers, Ryan M. and Mendis, Gamini P. and Jayakody, Lahiru N.},
|
||||
title = {Engineered Pseudomonas putida monoculture system for green synthesis of 7-methylxanthine},
|
||||
journal = {Green Chemistry},
|
||||
volume = {27},
|
||||
number = {37},
|
||||
pages = {11365-11379},
|
||||
year = {2025},
|
||||
month = {10},
|
||||
abstract = { 7-Methylxanthine (7-MX) is a clinically proven safe drug to treat myopia. The chemical synthesis of 7-MX is hindered due to low specificity, demanding sustainable biological production using renewable, cost-effective feedstocks. To this end, we systematically engineered robust P. putida EM42 to produce 7-MX using caffeine and glycerol in minimal salt media. Removing the transcriptional repressor (glpR), genome integration of heterologous N-demethylase and its reductase, ndmABD, and overexpression of native fdhA to balance the redox cofactors enabled the selective conversion of caffeine to 7-MX with 100\% yield. We discovered a native transporter, PP\_RS18750, that efficiently takes up caffeine, facilitating the conversion in glycerol-containing media. We achieved 9.2 ± 0.42 g L−1 of 7-MX in a 3-L bioreactor by process-level optimization, the highest titer reported to date. Our techno-economic analysis indicates that this novel engineered monoculture approach can produce pharmaceutical-grade 7-MX commercially for \$328 per kg, with remarkably low E-factor and Process Mass Intensity (PMI) values, demonstrating the sustainable green valorization of caffeine into high-value methylated xanthine. },
|
||||
issn = {1463-9262},
|
||||
doi = {10.1039/d5gc02883c},
|
||||
url = {https://doi.org/10.1039/d5gc02883c},
|
||||
eprint = {https://pubs.rsc.org/gc/article-pdf/27/37/11365/10400487/d5gc02883c.pdf},
|
||||
}
|
||||
@article{theobrominnoMenmr,
|
||||
author = {Bouzková, Kateřina and Babinský, Martin and Novosadová, Lucie and Marek, Radek},
|
||||
title = {Intermolecular Interactions in Crystalline Theobromine
|
||||
as Reflected in Electron Deformation Density and 13C NMR
|
||||
Chemical Shift Tensors},
|
||||
journal = {Journal of Chemical Theory and Computation},
|
||||
volume = {9},
|
||||
number = {6},
|
||||
pages = {2629-2638},
|
||||
year = {2013},
|
||||
month = {06},
|
||||
abstract = {An understanding of the role of intermolecular
|
||||
interactions in
|
||||
crystal formation is essential to control the generation of diverse
|
||||
crystalline forms which is an important concern for pharmaceutical
|
||||
industry. Very recently, we reported a new approach to interpret the
|
||||
relationships between intermolecular hydrogen bonding, redistribution
|
||||
of electron density in the system, and NMR chemical shifts (Babinský
|
||||
et al. J. Phys. Chem. A, 2013, 117, 497). Here, we employ this approach to characterize
|
||||
a full set of crystal interactions in a sample of anhydrous theobromine
|
||||
as reflected in 13C NMR chemical shift tensors (CSTs).
|
||||
The important intermolecular contacts are identified by comparing
|
||||
the DFT-calculated NMR CSTs for an isolated theobromine molecule and
|
||||
for clusters composed of several molecules as selected from the available
|
||||
X-ray diffraction data. Furthermore, electron deformation density
|
||||
(EDD) and shielding deformation density (SDD) in the proximity of
|
||||
the nuclei involved in the proposed interactions are calculated and
|
||||
visualized. In addition to the recently reported observations for
|
||||
hydrogen bonding, we focus here particularly on the stacking interactions.
|
||||
Although the principal relations between the EDD and CST for hydrogen
|
||||
bonding (HB) and stacking interactions are similar, the real-space
|
||||
consequences are rather different. Whereas the CHX
|
||||
hydrogen bonding influences predominantly and significantly the in-plane
|
||||
principal component of the 13C CST perpendicular to the
|
||||
HB path and the CH hydrogen bonding modulates
|
||||
both in-plane components of the carbonyl 13C CST, the stacking
|
||||
modulates the out-of-plane electron density resulting in weak deshielding
|
||||
(2–8 ppm) of both in-plane principal components of the CST
|
||||
and weak shielding (ca. 5 ppm) of the out-of-plane component.
|
||||
The hydrogen-bonding and stacking interactions may add to or subtract
|
||||
from one another to produce total values observed experimentally.
|
||||
On the example of theobromine, we demonstrate the power of this approach
|
||||
to identify and classify the intermolecular forces that govern the
|
||||
packing motifs in crystals and modulate the NMR CSTs.},
|
||||
issn = {1549-9618},
|
||||
doi = {10.1021/ct400209b},
|
||||
url = {https://doi.org/10.1021/ct400209b},
|
||||
eprint = {https://pubs.acs.org/jctcce/article-pdf/9/6/2629/8808212/ct400209b.pdf},
|
||||
}
|
||||
@article{theobrominnmr,
|
||||
author = {Thevis, Mario and Opfermann, Georg and Krug, Oliver and Schänzer, Wilhelm},
|
||||
title = {Electrospray ionization mass spectrometric characterization and quantitation of xanthine derivatives using isotopically labelled analogues: an application for equine doping control analysis},
|
||||
journal = {Rapid Communications in Mass Spectrometry},
|
||||
volume = {18},
|
||||
number = {14},
|
||||
pages = {1553-1560},
|
||||
doi = {https://doi.org/10.1002/rcm.1518},
|
||||
url = {https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/abs/10.1002/rcm.1518},
|
||||
eprint = {https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/pdf/10.1002/rcm.1518},
|
||||
abstract = {Abstract Isotope-dilution mass spectrometry has been employed successfully in numerous fields of analytical chemistry enabling the establishment of fast and reliable procedures. In equine sports, xanthine derivatives such as caffeine and theobromine are prohibited, and doping control laboratories analyze horse urine specimens regarding these illicit performance-enhancing drugs. Theobromine has to exceed a threshold level of 2 μg/mL, hence a robust and reliable quantitation is required. Stably deuterated theobromine and caffeine were synthesized by the reaction of xanthine or theobromine with iodomethane-d3 in the presence of N-methyl-N-trimethylsilyltrifluoroacetamide or potassium carbonate in acetonitrile, respectively. Both compounds were characterized by nuclear magnetic resonance spectroscopy and electrospray ionization tandem mass spectrometry, and a robust and fast assay for the qualitative and quantitative analysis of theobromine in equine urine samples was validated. Urine specimens were extracted by means of solid-phase extraction cartridges, and concentrated extracts were analyzed by liquid chromatography interfaced to a triple-quadrupole mass spectrometer. In addition, the dissociation behavior of deuterated analogues to caffeine and theobromine allowed proposals for fragmentation routes of xanthine derivatives after atmospheric pressure ionization and collisionally activated dissociation. Copyright C 2004 John Wiley and Sons, Ltd.},
|
||||
year = {2004}
|
||||
}
|
||||
@article{cinamnmr,
|
||||
title = {A comparative vibrational and NMR study of cis-cinnamic acid polymorphs and trans-cinnamic acid},
|
||||
journal = {Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy},
|
||||
volume = {57},
|
||||
number = {3},
|
||||
pages = {513-519},
|
||||
year = {2001},
|
||||
issn = {1386-1425},
|
||||
doi = {https://doi.org/10.1016/S1386-1425(00)00401-7},
|
||||
url = {https://www.sciencedirect.com/science/article/pii/S1386142500004017},
|
||||
author = {Kazuhiko Hanai and Akio Kuwae and Takatomo Takai and Hitoshi Senda and Ko-Ki Kunimoto},
|
||||
keywords = {-Cinnamic acid, -Cinnamic acid, Polymorphism, IR/Raman spectra, NMR spectra},
|
||||
abstract = {The IR and Raman spectra of the two polymorphic forms (58°- and 68°-forms) of cis-cinnamic acid were measured, and the spectral differences discussed on the basis of the crystal structures of the two forms. The IR bands related to the COOH group differ in the frequencies and band shape, reflecting differences in the hydrogen bonding between the two modifications. These spectra were compared with those of trans-cinnamic acid. The IR, Raman, and NMR spectra of the isotopic compounds, including the deuterated and 13C analogs of the cis and trans acids, were also recorded in the solid state and in solution to confirm the spectral assignments.}
|
||||
}
|
||||
@article{mcoumnmr,
|
||||
author = {Nakazawa, Takahiro and Ohsawa, Keisuke},
|
||||
title = {Metabolism of Rosmarinic Acid in Rats},
|
||||
journal = {Journal of Natural Products},
|
||||
volume = {61},
|
||||
number = {8},
|
||||
pages = {993-996},
|
||||
year = {1998},
|
||||
month = {08},
|
||||
abstract = {The urine of rats administered rosmarinic acid (7) orally contained seven metabolites, which
|
||||
were identified as trans-caffeic acid 4-O-sulfate (1), trans-m-coumaric acid 3-O-sulfate (2), trans-ferulic acid 4-O-sulfate (3), trans-caffeic acid (4), m-hydroxyphenylpropionic acid (5), trans-m-coumaric acid (6), and unchanged rosmarinic acid (7) by spectroscopic and chemical data. The
|
||||
total cumulative amount of 1−7 excreted in the urine 48 h after the oral administration of
|
||||
rosmarinic acid was approximately 31.8 Percent of the dose administered. On the other hand, the
|
||||
metabolites attributed to rosmarinic acid could not be found in the bile. Orally administered
|
||||
rosmarinic acid may thus be concluded to be excreted in the urine rather than in the bile, with
|
||||
cleavage of ester bonds, selective para-dehydroxylation, methylation, and sulfate-conjugation.
|
||||
Metabolites 2, 3, 5, and 6 were also detected in the plasma. },
|
||||
issn = {0163-3864},
|
||||
doi = {10.1021/np980072s},
|
||||
url = {https://doi.org/10.1021/np980072s},
|
||||
eprint = {https://pubs.acs.org/jnprdf/article-pdf/61/8/993/13045095/np980072s.pdf},
|
||||
}
|
||||
@article{pcoumnmr,
|
||||
author = {Świsłocka, Renata and Kowczyk-Sadowy, Małgorzata and Kalinowska, Monika and Lewandowski, Włodzimierz},
|
||||
title = {Spectroscopic (FT-IR, FT-Raman, 1H and 13C NMR) and theoretical studies of p-coumaric acid and alkali metal p-coumarates},
|
||||
journal = {Journal of Spectroscopy},
|
||||
volume = {27},
|
||||
number = {1},
|
||||
pages = {546146},
|
||||
keywords = {p-Coumaric acid, alkali metal p-coumarates, IR, Raman, NMR spectra},
|
||||
doi = {https://doi.org/10.3233/SPE-2012-0568},
|
||||
url = {https://onlinelibrary.wiley.com/doi/abs/10.3233/SPE-2012-0568},
|
||||
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.3233/SPE-2012-0568},
|
||||
abstract = {The evaluation of the electronic charge distribution in metal complexes enables more precise interpretation of mechanism by which particular metal ions affect biochemical properties of ligands [J. Inorg. Biochem. 99 (2005), 1407–1423, J. Mol. Struct. 919 (2009), 284–289]. In this paper we investigated the influence of alkali metal cations (lithium, sodium, potassium, rubidium and cesium) on the electronic structure of p-coumaric acid (p-CA). It allowed to observe the systematic changes in the spectra of investigated complexes depending on the position of the element in the periodic table. p-Coumaric acid is a derivative of cinnamic acid that occurs in several plant species. Li, Na, K, Rb and Cs p-coumarates were synthesized and the experimental and theoretical FT-IR, FT-Raman, 1H and 13C NMR spectra of p-coumaric acid and its salts were registered and analyzed. The structures, atomic charges, infrared and NMR spectra of p-coumaric acid and Li, Na, K salts were calculated by B3LYP/6-311++G** method.},
|
||||
year = {2012}
|
||||
}
|
||||
@article{aldhnmr,
|
||||
author = {Kuan, Fu-Hua and Inoue, Yoshio and Chûjô, Riichiro},
|
||||
title = {Structure and molecular dynamics of solid-state inclusion complexes of cyclodextrin and permethylated cyclodextrin with benzaldehyde studied by high-resolution CP/MAS13C NMR},
|
||||
journal = {Journal of inclusion phenomena},
|
||||
volume = {4},
|
||||
number = {3},
|
||||
pages = {281–290},
|
||||
doi = {https://doi.org/10.1007/BF00658002},
|
||||
eprint = {https://link.springer.com/article/10.1007/BF00658002},
|
||||
abstract = {The structure and molecular dynamics of the benzaldehyde inclusion-complexes with alpha-andbeta-cyclodextrins and permethylated alpha-cyclodextrin in the solid state have been studied by high-resolution cross-polarization/magic angle sample-spinning13C NMR spectroscopy. It is shown that the guest benzaldehyde molecule undergoes motion in the host cyclodextrin cavity and the rate of motion depend on the cavity size. In the alpha-cyclodextrin complex, compared to beta-and permethylated alpha-cyclodextrin complexes, the benzaldehyde motion is severely restricted, but under high-vacuum benzaldehyde is released more easily from the cavity.},
|
||||
year = {1986}
|
||||
}
|
||||
@Article{caffacdnmr,
|
||||
AUTHOR = {Yu, Jiahui and Xie, Jingchen and Sun, Miao and Xiong, Suhui and Xu, Chunfang and Zhang, Zhimin and Li, Minjie and Li, Chun and Lin, Limei},
|
||||
TITLE = {Plant-Derived Caffeic Acid and Its Derivatives: An Overview of Their NMR Data and Biosynthetic Pathways},
|
||||
JOURNAL = {Molecules},
|
||||
VOLUME = {29},
|
||||
YEAR = {2024},
|
||||
NUMBER = {7},
|
||||
ARTICLE-NUMBER = {1625},
|
||||
URL = {https://www.mdpi.com/1420-3049/29/7/1625},
|
||||
PubMedID = {38611904},
|
||||
ISSN = {1420-3049},
|
||||
ABSTRACT = {In recent years, caffeic acid and its derivatives have received increasing attention due to their obvious physiological activities and wide distribution in nature. In this paper, to clarify the status of research on plant-derived caffeic acid and its derivatives, nuclear magnetic resonance spectroscopy data and possible biosynthetic pathways of these compounds were collected from scientific databases (SciFinder, PubMed and China Knowledge). According to different types of substituents, 17 caffeic acid and its derivatives can be divided into the following classes: caffeoyl ester derivatives, caffeyltartaric acid, caffeic acid amide derivatives, caffeoyl shikimic acid, caffeoyl quinic acid, caffeoyl danshens and caffeoyl glycoside. Generalization of their 13C-NMR and 1H-NMR data revealed that acylation with caffeic acid to form esters involves acylation shifts, which increase the chemical shift values of the corresponding carbons and decrease the chemical shift values of the corresponding carbons of caffeoyl. Once the hydroxyl group is ester, the hydrogen signal connected to the same carbon shifts to the low field (1.1~1.6). The biosynthetic pathways were summarized, and it was found that caffeic acid and its derivatives are first synthesized in plants through the shikimic acid pathway, in which phenylalanine is deaminated to cinnamic acid and then transformed into caffeic acid and its derivatives. The purpose of this review is to provide a reference for further research on the rapid structural identification and biofabrication of caffeic acid and its derivatives.},
|
||||
DOI = {10.3390/molecules29071625}
|
||||
}
|
||||
@article{mhydaldhnmr,
|
||||
author = {Mart, H. and Sökmen, T. and Yürük, H.},
|
||||
title = {The synthesis and thermal properties of oligo-3-hydroxybenzaldehyde synthesized by oxidative polycondensation},
|
||||
journal = {Journal of Applied Polymer Science},
|
||||
volume = {101},
|
||||
number = {2},
|
||||
pages = {892-897},
|
||||
keywords = {oxidative polycondensation, polyaromatics, polyphenols, oligomers},
|
||||
doi = {https://doi.org/10.1002/app.23537},
|
||||
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/app.23537},
|
||||
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/app.23537},
|
||||
abstract = {Abstract Polymerization of 3-hydroxybenzaldehyde was investigated by oxidative polycondensation (OP) method. No polycondensation reaction was observed both in acidic (in CH3COOH) and organic (in THF) media. Polycondensation was carried out with hydrogenperoxide (H2O2) in an aqueous alkaline medium at 90°C. The product was characterized by 1H NMR, 13C NMR, FTIR, UV–vis, and elemental analysis. The number average molecular weight, mass average molecular weight, and polydispersity index values of O-3HBA were found to be 3600, 8000 g mol−1, and 2.22, respectively. The product (O-3HBA) with reactive aldehyde and hydroxyl group was soluble in most polar organic solvents and was composed of phenylene units. Thermal properties of the oligomer were investigated by thermogravimetric analyses under an air atmosphere. The weight loss of O-3HBA was found to be 5 and 50 Percent at 231 and >1000C, respectively. The carboneous residue of the O-3HBA was 54 Percent at 1000C. C 2006 Wiley Periodicals, Inc. J Appl Polym Sci 101: 892–897, 2006},
|
||||
year = {2006}
|
||||
}
|
||||
@article{phydaldhnmr,
|
||||
author = {Jha, Anjali and Kumar, B.Rajesh and Kumar Ch, RaviShankar},
|
||||
title = {Synthesized Novel Schiff Base of 4-Hydroxybenzaldehyde with Anilines for Optoelectronic
|
||||
Applications},
|
||||
journal = {SSRN Preprint Server},
|
||||
pages = {46},
|
||||
keywords = {Schiff base, Spectral studies, Computational studies, Energy gap, Refractive index.},
|
||||
url = {https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4934411},
|
||||
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/app.23537},
|
||||
abstract = {Optical materials organic in nature are leading materials exhibiting semiconducting properties is trend of present technology in optical and electronic applications. Active organic materials of Schiff bases are of vital importance in terms of their molecular properties, band gap, refractive index and dielectric operated at room temperature than compared to inorganic materials at elevated temperatures during synthesis. The present article focuses on the development of thin films with the synthesis of Schiff base of 4-hydroxy benzaldehydes and substituted anilines using the green synthesis method. The formation of the Schiff base compounds was confirmed with spectroscopic methods with shifts in wavenumbers in infrared spectra, transition with optical band gap with ultraviolet spectra and chemical environment with chemical shifts using proton NMR. Powdered XRD provide information of structure, composition and crystalline proximity of the synthesized Schiff base compounds. Optical properties refractive index and dielectric constant were attributed with spectroscopic ellipsometer. Computational studies were performed using the Gaussian 16 package with the B3LYP method basis set 6-311++** for all molecular compounds to confirm the molecular structures, optimized geometry, and electronic and optical properties. The insights of these properties are best visualized in terms of quantum mechanical descriptors responsible due to changes in electron density. Studies of these Schiff base compounds with nitro groups proved to exhibit optical properties and as an excellent organic semiconducting material with an energy gap of 3.08 eV; refractive index of 2.074, and dielectric constant of 4.303. },
|
||||
year = {2024}
|
||||
}
|
||||
@article{mphydaldhnmr,
|
||||
author = {Syfani, Nova and Putra, Deddi Prima and Arbani, Dayar},
|
||||
title = {3,4-DIHYDROXYBENZOIC ACID AND 3,4-DIHYDROXYBENZALDEHYDE FROM THE FERN
|
||||
Trichomanes chinense L.; ISOLATION, ANTIMICROBIAL AND ANTIOXIDANT PROPERTIES},
|
||||
journal = {Indo. J. Chem.,},
|
||||
volume = {12},
|
||||
number = {3},
|
||||
pages = {273-278},
|
||||
keywords = {Trichomanes chinense L.; 3,4-dihydroxybenzoic acid; 3,4-dihydroxybenzaldehyde; antioxidant;
|
||||
antimicrobial},
|
||||
url = {https://academia-edu-documents.ada3b51d29be5ae5c31d26340608fd48.r2.cloudflarestorage.com/76337429/62cb66d00830376d6243dfc70e9c9c13f07a-libre.pdf?response-content-disposition=inline%3B%20filename%3D3_4_DIHYDROXYBENZOIC_ACID_AND_3_4_DIHYDR.pdf&response-content-type=application%2Fpdf&X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=62bb68dcc7da7de029ac4fdac624cee9%2F20261018%2Fauto%2Fs3%2Faws4_request&X-Amz-Date=20261018T014804Z&X-Amz-Expires=3600&X-Amz-SignedHeaders=host&X-Amz-Signature=2d857d9fd2556313a486db1447aa14a97dca8a72ac8aa120ff8d3c255860bd06},
|
||||
abstract = {3,4-dihydroxybenzoic acid (1) and 3,4-dihydroxybenzaldehyde (2) have been isolated from ethyl acetate
|
||||
fraction of methanolic fractions of leaves, stems and roots of the fern Trichomanes chinense L. (Hymenophyllaceae).
|
||||
These two compounds also showed significant antioxidant using DPPH and antimicrobial activities using the disc
|
||||
diffusion assay.},
|
||||
year = {2012}
|
||||
}
|
||||
@article{heavyateff1,
|
||||
author = {Lodewyk, Michael W. and Siebert, Matthew R. and Tantillo, Dean J.},
|
||||
title = {Computational Prediction of 1H and 13C Chemical Shifts: A Useful Tool for Natural Product, Mechanistic, and Synthetic Organic Chemistry},
|
||||
journal = {Chemical Reviews},
|
||||
volume = {112},
|
||||
number = {3},
|
||||
pages = {1839-1862},
|
||||
year = {2012},
|
||||
month = {03},
|
||||
issn = {0009-2665},
|
||||
doi = {10.1021/cr200106v},
|
||||
url = {https://doi.org/10.1021/cr200106v},
|
||||
eprint = {https://pubs.acs.org/chreay/article-pdf/112/3/1839/8644981/cr200106v.pdf},
|
||||
}
|
||||
@article{heavyatef2,
|
||||
author = {Jonas, Eric and Kuhn, Stefan and Schlörer, Nils},
|
||||
title = {Prediction of chemical shift in NMR: A review},
|
||||
journal = {Magnetic Resonance in Chemistry},
|
||||
volume = {60},
|
||||
number = {11},
|
||||
pages = {1021-1031},
|
||||
keywords = {chemical shift prediction, graph neural network, machine learning, NMR},
|
||||
doi = {https://doi.org/10.1002/mrc.5234},
|
||||
url = {https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/abs/10.1002/mrc.5234},
|
||||
eprint = {https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/pdf/10.1002/mrc.5234},
|
||||
abstract = {Abstract Calculation of solution-state NMR parameters, including chemical shift values and scalar coupling constants, is often a crucial step for unambiguous structure assignment. Data-driven (sometimes called empirical) methods leverage databases of known parameter values to estimate parameters for unknown or novel molecules. This is in contrast to popular ab initio techniques that use detailed quantum computational chemistry calculations to arrive at parameter estimates. Data-driven methods have the potential to be considerably faster than ab inito techniques and have been the subject of renewed interest over the past decade with the rise of high-quality databases of NMR parameters and novel machine learning methods. Here, we review these methods, their strengths and pitfalls, and the databases they are built on.},
|
||||
year = {2022}
|
||||
}
|
||||
@article{nmrbinsize,
|
||||
author = {Schripsema, Jan},
|
||||
title = {Similarity and differential NMR spectroscopy in metabolomics: application to the analysis of vegetable oils with 1H and 13C NMR},
|
||||
journal = {Metabolomics},
|
||||
volume = {15},
|
||||
number = {39},
|
||||
pages = {1573-3890},
|
||||
doi = {https://doi.org/10.1007/s11306-019-1502-9},
|
||||
abstract = {In NMR based metabolomics there is a need for tools to easily compare spectra and to extract the maximum of information from the data.},
|
||||
year = {2019}
|
||||
}
|
||||
@article{olefinmetathese,
|
||||
author = {Connon, Stephen J. and Blechert, Siegfried},
|
||||
title = {Recent Developments in Olefin Cross-Metathesis},
|
||||
journal = {Angewandte Chemie International Edition},
|
||||
volume = {42},
|
||||
number = {17},
|
||||
pages = {1900-1923},
|
||||
keywords = {cross-metathesis, homogeneous catalysis, olefins, ring-opening metathesis, synthetic methods},
|
||||
doi = {https://doi.org/10.1002/anie.200200556},
|
||||
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/anie.200200556},
|
||||
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/anie.200200556},
|
||||
abstract = {Abstract Among the many types of transition-metal-catalyzed CC bond-forming reactions, olefin metathesis has come to the fore in recent years owing to the wide range of transformations that are possible with commercially available and easily handled catalysts. Consequently, olefin metathesis is now widely considered as one of the most powerful synthetic tools in organic chemistry. Until recently the intermolecular variant of this reaction, cross-metathesis, had been neglected despite its potential. With the evolution of new catalysts, the selectivity, efficiency, and functional-group compatibility of this reaction have improved to a level that was unimaginable just a few years ago. These advances, together with a better understanding of the mechanism and catalyst–substrate interactions, have brought us to a stage where more and more researchers are employing cross-metathesis reactions in multistep procedures and in the synthesis of natural products. The recent inclusion of alkynes and hindered bicyclic olefins as viable substrates for bimolecular metathesis coupling, the discovery of enantioselective cross-metathesis and cross-metathesis in water, and the successful marriage of metathesis and solid-phase organic synthesis has further widened the scope of this versatile reaction.},
|
||||
year = {2003}
|
||||
}
|
||||
@article{dielsalder,
|
||||
author = {Sauer, Jürgen and Wiest, Hubert and Mielert, Albrecht},
|
||||
title = {Eine Studie der DIELS-ALDER-Reaktion, I. Die Reaktivität von Dienophilen gegenüber Cyclopentadien und 9.10-Dimethyl-anthracen},
|
||||
journal = {Chemische Berichte},
|
||||
volume = {97},
|
||||
number = {11},
|
||||
pages = {3183-3207},
|
||||
doi = {https://doi.org/10.1002/cber.19640971129},
|
||||
url = {https://chemistry-europe.onlinelibrary.wiley.com/doi/abs/10.1002/cber.19640971129},
|
||||
eprint = {https://chemistry-europe.onlinelibrary.wiley.com/doi/pdf/10.1002/cber.19640971129},
|
||||
abstract = {Abstract Die Additionsgeschwindigkeiten verschiedener Dienophile an Cyclopentadien und 9.10-Dimethyl-anthracen werden in wasserfreiem Dioxan als Solvens durch kinetische Messungen ermittelt und in Hinsicht auf den Mechanismus der DIELS-ALDER-Reaktion diskutiert.},
|
||||
year = {1964}
|
||||
}
|
||||
@article{ringstrain,
|
||||
author = {Wiberg, Kenneth B.},
|
||||
title = {The Concept of Strain in Organic Chemistry},
|
||||
journal = {Angewandte Chemie International Edition in English},
|
||||
volume = {25},
|
||||
number = {4},
|
||||
pages = {312-322},
|
||||
keywords = {Strained molecules},
|
||||
doi = {https://doi.org/10.1002/anie.198603121},
|
||||
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/anie.198603121},
|
||||
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/anie.198603121},
|
||||
abstract = {Abstract “Die Ringschließung ist offenbar diejenige Erscheinung, welche am meisten über die räumliche Anordnung der Atome Auskunft geben kann. Wenn eine Kette von 5 und 6 Gliedern sich leicht, eine von weniger oder mehr Gliedern sich schwierig oder auch gar nicht schließen läßt, so müssen dafür offenbar räumliche Gründe vorhanden sein.… Die vier Valenzen des Kohlenstoffatoms wirken in den Richtungen, welche den Mittelpunkt der Kugel mit den Tetraederecken verbinden, und welche miteinander einen Winkel von 109°28′ machen. Die Richtung der Anziehung kann eine Ablenkung erfahren, die jedoch eine mit der Größe der Letzteren wachsende Spannung zur Folge hat,”[ Ring formation is evidently the reaction that can provide the most important information on the spatial arrangement of atoms. Steric reasons should explain the observation that 5- or 6-membered chain undergoes ready closure, whereas a shorter or longer chain undergoes difficult or no closure.… The four valences of the carbon atom act in the directions that connect the center of a sphere with the corners of a tetrahedron and form angles of 109°28′ with one another. The direction of the attraction can deviate, but this in increasing strain as the sizes of the latter increase. ] This is the quintessence of the “ring-strain theory” formulated by Adolf von Baeyer over one hundred years ago. Although it is today only one facet of the many aspects of strain theory, it has repeatedly stimulated experimental and theoretical chemists. Among the most spectacular of the recent successes in synthetic chemistry are the syntheses of tetra-tert-butyltetrahedrane and [1.1.1]propellane. The reasons for the great stability of these two highly strained compounds are completely different. The experimental findings as well as the results of theoretical analysis by means of molecular mechanics and ab initio calculations have contributed decisively to our present state of knowledge of the structure, energy, and reactivity of organic compounds.},
|
||||
year = {1986}
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
Reference in New Issue
Block a user