DOI: 10.57745/cbupp3
title: Manipulation of a cyclodextrin-ferrociphenol supramolecular models database using a web application

description: Content Diverse data about modeling of a cyclodextrin-ferrociphenol supramolecular assemblage. Starting from the best models calculated with different simple CD, 21 oxygen atoms were modified (called "mutations") giving 21 derived models). The best one was selected to do the same, creating tree of modellings/mutations. For models with one CD, 10 series were created and for models with 2 CD 4 series. The related published article (Int. J. Mol. Sci. 2023, 24, 15, 12288. (open access) https://doi.org/10.3390/ijms241512288) shows that uncommon hydrogen bonds (simple or clamp) can be formed between the iron atom of ferrocene of ferrociphenol and one or two OH of the cyclodextrin (see the graphical abstract of the article in this dataset, file GA.jpeg). To the best of our knowledge, this is the first time that it has been described by modelling in supramolecular systems involving ferrocene and a cyclodextrin. The ferrociphenol (somethimes called ferrocifen) is SuccFerr (also known as P722) and have shown very good IC50 on certain cancer cells, for example 0.035 µM on Triple Negative Breast Cancer (MDA-MB-231) and on Ovarian Cancer A2780. On Ovarian Cancer A2780-Cis (resistant to Cis-platin) the IC50 is 0.049 µM: J. Med. Chem. 2017, 60, 8358-8368 All ferrociphenols seem to act by oxidation into the cells, forming very reactive species called quinone methides: Angew. Chem. Int. Ed. 2009, 48, 9124-9126. These quinone methides can form adducts with some proteins, on their cystein or selenocystein amino acids: Angew. Chem. Int. Ed. 2016, 55, 10431-10434 (free access on Hal). SuccFerr has a particularity: Its quinone methide is stabilized by a lone pair - π interaction that seems to permit it to reach its target into the cell: Angew. Chem. Int. Ed. 2019, 58, 8421-8425 (free access on Hal) However, SuccFerr is lipophilic and has a very low solubility in water, so a formulation is needed, using: lipid nanocapsules (LNCs): Int. J. Pharm. 2022, 626, 122164 (free access on Hal), or Langmuir 2023, 39, 5, 1885-1896 (free access on Hal) Cyclodextrins (subject of this dataset): Molecules 2022, 14, 4651 (open access) This dataset is focused on modelling on SuccFerr-cyclodextrin supramolecular assemblages. The structure of SuccFerr and the 4 moieties that can be inserted into a cyclodextrin can be seen in the furnished picture "SuccFerr-RDG.jpg". The publication related to this dataset is: Pascal Pigeon, Feten Najlaoui, Michael James McGlinchey, Juan Sanz García, Gérard Jaouen, Stéphane Gibaud, Unravelling the Role of Uncommon Hydrogen Bonds in Cyclodextrin Ferrociphenol Supramolecular Complexes: A Computational Modelling and Experimental Study, Int. J. Mol. Sci. 2023, 24, 15, 12288. (open access) https://doi.org/10.3390/ijms241512288. This article belongs to the Special Issue "Cyclodextrins: Properties and Applications" that belongs to the section "Macromolecules" of International Journal of Molecular Sciences. GA.jpeg is the graphical abstract that show the uncommon hydrogen bonds between Fe and OH of CD. See README.txt file for detail. Note: In the article (Int. J. Mol. Sci.), ΔrH° was replaced by ΔE, but the meaning is the same. Database and export as CSV/TAB files : CSV/tab file containing the table calculscd of the database for 1-CD models: calculscd.tab CSV/tab file containing the table calculs2cd of the database for 2-CD models: calculs2cd.tab CSV/tab file containing the table cdxcd of the database for 36 combinations of 2-CD models for series 2-CD S4: cdxcd.tab Other version of the calculscd.tab but with tab as separators and without quotation marks enclosing the Columns, used for the C program to work properly: calculscdprog.tab Other version of the calculs2cd.tab but with tab as separators and without quotation marks enclosing the Columns, used for the C program to work properly: calculs2cdprog.tab JSON file containing all the database (tables calculscd, calculs2cd and cdxcd) in JSON format: pascal.json XML file containing all the database (tables calculscd, calculs2cd and cdxcd) in XML format: pascal.xml sql file containing all the database (tables calculscd, calculs2cd and cdxcd) in SQLformat. This is this file that should be used to import all the database into a database management software (as MySQL/ MariaDB, ...) since it also contains the constraints on keys (unicity, index, autoincrement): pascal.sql Models zip archive containing 13261 XYZ files (models in XYZ format classified by number of series). They were created by Spartan, but were corrected by the C program (removal of Lig atoms (confused with lithium on other software), addition of the missing two first lines, reduction of size (spaces replaced by tab)): XYZ.zip zip archive containing 4 XYZ files describing 4 special models calculated in DFT (DFT calculation on the best model of series 1-CD S2 in water: best 1-CD series 2 DFT water.xyz, DFT calculation on the best model of series 1-CD S8 in vacuum: best 1-CD series 8 DFT vacuum.xyz, DFT calculation on the best model of series 1-CD S8 in water: best 1-CD series 8 DFT water.xyz, DFT calculation of ferrocene and MeOH: Fc + MeOH DFT.xyz): DFT.zip 28 files in Spartan original format contening models + modelling parameters + modelling results for some 1-CD and 2-CD series (two for each 1-CD Sy and 2-CD Sy series, where y = series number). The format for the file names is : x-CD-Sy-G0-ID-z.spartan (for the G0 models) and x-CD-Sy-best-ID-z.spartan (for the best models) where x = 1 (for 1-CD models) or 2 (for 2-CD models), y is the series and z is the ID (key/number of model in the database/tab file). XYZ file computed with Gaussian 16 on the supercomputer MeSU (SACADO) (Sorbonne Université) for the best model of series 1-CD series 8 (ID 7759) with wB97XD functional with the 6-311G(d,p) basis set (including a set of p polarization functions for the hydrogen atoms, and a set of d polarization functions for the second-row elements): S8_DFT_opt_geom.xyz. Results zip archive containing 13247 webpages describing the models : - HTML files generated by the C program (1-CD-webpage-ID-1.html to 1-CD-webpage-ID-9767.html and 2-CD-webpage-ID-1.html to 2-CD-webpage-ID-3458.html) and TableofHbondsbySeries-1CD.html and TableofHbondsbySeries-2CD.html). - HTML files needed for the C program to work : (beginningwebpage1CD.html and beginningwebpage2CD.html and stats1CDS1.html to stats1CDS10.html and stats2CDS1.html to stats2CDS4.html). - HTML files manually saved and modified (Statisticsonallseries1CD.html and Statisticsonallseries2CD.html and CDxCD.html and StatisticsonallCD.html): webpages.zip Text file describing special H bonds for each 1-CD model : Hbonds-1CD.txt Text file describing special H bonds for each 2-CD model : Hbonds-2CD.txt Programs to manage the data collect PHP pages cdmodele.php, cdmodele2cd.php, CDxCD.php and functions.inc to run the web application used to collect the data and to do some stats. This program (named CDModelTree) was deposited at https://hal.science/hal-03991394 in association with Software Heritage. Needs a sofware as XAMPP to run program in C (source code) to analyse the XYZ files for 1-CD and 2-CD models (need calculscdprog.csv or calculs2cdprog.csv to work and should be compilated). It also needs the folder structure containing the orginal XYZ files to convert (not furnished). Thus, it will not find these files (but given for information). It was created using Code::Blocks: analysisofmodels.c Images to illustrate Figure describing the numbering of the 21 important oxygen atoms of the cyclodextrins used in this study (Oi of the database): Cyclodextrin-numbering-DRG.tif Structure of SuccFerr (P722) and the 4 moieties than can be inserted into a cyclodextrin: SuccFerr-RDG.jpg Graphical abstract of the article in International Journal of Molecular Sciences, showing the appearance of the clamp between Fe and two OH of the CD when removing methylation on O20: GA.jpeg Artistic representation of a tree of modifications of the models done in this work. It shows the molecule (one of its moieties, as in the logo of this dataset) inserted into a cyclodextrin (CD). The methylation state of all oxygen atoms the CD (blue or green spheres = H or Me) for each generation is inverted (last change is the red sphere, only the best model, selected to continue the tree, is shown). The increase of stability is represented by the molecule going deeper into the CD. If the stability decreased (shallow insertion, dead end, model shown for illustration close to the "dead end" panel), a better model is choosen to continue the tree to go towards better models. Graphic created in 3D with Blender V3.0.1: TreeRDG.jpg Flowchart of the PHP program (cdmodele.php + cdmodele2cd.php + functions.inc): Figure-Flowchart-PHP-Program.tif Bitmap files (.bmp), having a name in x-CD-Sy-best-ID-z.bmp, where x = 1 (1-CD series) or 2 (2-CD series), y = the series, z = the ID of the model, represent the 2D display (image of the 2D projection) saved from the 3D model from Spartan 14. Some hydrogen bonds are displayed. Logo of this dataset. Represents a moiety of a molecule as SuccFerr (red sphere) inserted into a cyclodextrin (very schematic). Done in 3D with Blender V3.0.1: logo.jpg.