The NIST Chemical Kinetics Database includes essentially all reported kinetics results for thermal gas-phase chemical reactions. The database is designed to be searched for kinetics data based on the specific reactants involved, for reactions resulting in specified products, for all the reactions of a particular species, or for various combinations of these. In addition, the bibliography can be searched by author name or combination of names. The database contains in excess of 38,000 separate reaction records for over 11,700 distinct reactant pairs. These data have been abstracted from over 12,000 papers with literature coverage through early 2000. Rate constant records for a specified reaction are found by searching the Reaction Database. All rate constant records for that reaction are returned, with a link to 'Details' on that record. Each rate constant record contains the following information (as available): a) Reactants and, if defined, reaction products; b) Rate parameters: A, n, Ea/R, where k = A (T/298)*n exp[-(Ea/R)/T], where T is the temperature in Kelvins; c) Uncertainty in A, n, and Ea/R, if reported; d) Temperature range of experiment or temperature range of validity of a review or theoretical paper; e) Pressure range and bulk gas of the experiment; f) Data type of the record (i.e., experimental, relative rate measurement, theoretical calculation, modeling result, etc.). If the result is a relative rate measurement, then the reaction to which the rate is relative is also given; g) Experimental procedure, including separate fields for the description of the apparatus, the time resolution of the experiment, and the excitation technique. A majority of contemporary chemical kinetics methods are represented. The Kinetics Database is being expanded to include other resources for the convenience of the users. Presently this includes direct links to the corresponding NIST WebBook page for all substances for which such a link is possible. This is indicated by underling and highlighting the species. The WebBook provides thermodynamic, spectral, and other data on the species. Note that the link to the WebBook is opened as a new frame in your browser.

This reaction database is generated along with the manuscript "Comprehensive exploration of graphically defined reaction spaces".RGD1CHNO_AMsmiles.csv contains atom-mapped SMILES, activation energies, and enthalpies of formation for each reaction. RGD!_CHNO.h5 contains the geometry information and can be iterated by a python script from Github (https://github.com/zhaoqy1996/RGD1/parse_data.py). DFT_reaction_info.csv is supplied to reproduce figures in the article.RandP_smiles.txt is a dictionary to map the reactant and product smiles appear in RGD!_CHNO.h5 to a molecule index (molX).RGD1_RPs.h5 provides xtb and DFT optimized geometries of each individual reactant/product molecules. 3D ML models can be trained by combining RGD1_RPs.h5, RGD!_CHNO.h5, and RandP_smiles.txt (see https://github.com/zhaoqy1996/RGD1 for more details)IMPORTANT: We provided an UPDATED VERSION of RGD1 dataset in Ari 24, 2023. The initially posted version of the dataset reported swapped activation energies for ~24% of the forward/reverse reactions which were all corrected in this updated version.

This is the collection associated with list S73 MetXBioDB Metabolite Reaction Database from BioTransformer on the NORMAN Suspect List Exchange.

https://www.norman-network.com/nds/SLE/

This dataset is extracted from the database behind BioTransformer (http://biotransformer.ca/) by Yannick Djoumbou-Feunang, David S. Wishart and colleagues, for addition to the PubChem Transformations section. Change logs and version tracking at the ECI GitLab site.

Please cite the BioTransformer article when using this set: https://jcheminf.biomedcentral.com/articles/10.1186/s13321-018-0324-5

NOTE: This deposition is work in progress ...

Change log: 13 Oct: added InChIKey file. 16 Oct: updated substances with missing CIDs and transformations. 5/11 many bug fixes finally committed, added DTXSIDs. 22/6/2023 adjusted one CID that changed upon PubChem standardization. 15 Nov 2023: fixed typo in reaction description. 26 Feb 2024: corrected name for CID 65564. 6 Aug 2024: fixed many triazine synonyms.

Reactions extracted by text-mining from United States patents published between 1976 and September 2016. The reactions are available as CML or reaction SMILES. Note that the reactions SMILES are derived from the CML. The files can be unzipped using a program like 7-Zip.The reactions were extracted using an enhanced version of the reaction extraction code described in https://www.repository.cam.ac.uk/handle/1810/244727with LeadMine (https://www.nextmovesoftware.com/leadmine.html) used for chemical entity recognition.General tips:Duplicate reactions are frequent due to the same or highly similar text occurring in multiple patents, this is especially true when combining the applications and grant datasets, many reactions from applications will later appear in patent grants.Paragraph numbers are only present for 2005+ patent grants and patent applications.Multiple reactions can be extracted from the same paragraph.Atom maps in the reactions SMILES are derived using Epam's Indigo toolkit. While typically correct, the atom-maps are wrong in many cases and hence should not be entirely relied on.The reactions have been filtered to remove common cases of incorrectly extracted reactions:All product atoms must be accounted for by the atom-mappingThe product(s) must have >8 heavy atomsThe product must not be charged if it is a single componentThe number of products must be

KEGG LIGAND contains knowledge of chemical substances and reactions that are relevant to life. It is a composite database consisting of COMPOUND, GLYCAN, REACTION, RPAIR, and ENZYME databases, whose entries are identified by C, G, R, RP, and EC numbers, respectively. ENZYME is derived from the IUBMB/IUPAC Enzyme Nomenclature, but the others are internally developed and maintained. The primary database of KEGG LIGAND is a relational database with the KegDraw interface, which is used to generated the secondary (flat file) database for DBGET.

Comprehensive database of organic chemistry reactions with mechanisms, conditions, and examples

The NDRL/NIST Solution Kinetics Database contains data on rate constants for solution-phase chemical reactions. The database is designed to be searched by reactants, products, solvents, or any combination of these. In addition, the bibliography may be searched by author name, title words, journal, page(s), and/or year. This is not the same database as the one at Notre Dame, although both databases share a common data source.

A database based on the SABIO relational database that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. It aims to support modelers in the setting-up of models of biochemical networks, but it is also useful for experimentalists or researchers with interest in biochemical reactions and their kinetics. SABIO-RK contains and merges information about reactions such as reactants and modifiers, organism, tissue and cellular location, as well as the kinetic properties of the reactions. The type of the kinetic mechanism, modes of inhibition or activation, and corresponding rate equations are presented together with their parameters and measured values, specifying the experimental conditions under which these were determined. Links to other databases are provided for users to gather further information and to refer to the original publication. Information about reactions and their kinetic data can be exported to an SBML file. The reaction kinetics data are obtained by manual extraction from literature sources and curated.

Manually annotated reaction database where all reaction participants (reactants and products) are linked to the ChEBI database (Chemical Entities of Biological Interest) which provides detailed information about structure, formula and charge. Rhea provides built-in validations that ensure both elemental and charge balance of the reactions. The database has been populated with the reactions found in the Enzyme Commission (EC) list (and in the IntEnz and ENZYME databases), extending it with additional known reactions of biological interest. While the main focus of Rhea is enzyme-catalyzed reactions, other biochemical reactions are also included. Rhea is a manually annotated resource and it provides: stable reaction identifiers for each of its reactions; directionality information if the physiological direction of the reaction is known; the possibility to link several reactions together to form overall reactions; extensive cross-references to other resources including enzyme-catalyzed and other metabolic reactions, such as the EC list (in IntEnz), KEGG, MetaCyc and UniPathway; and chemical substructure and similarity searches on compounds in Rhea.

Link Function: information

Collection of reaction SMILES (reactants, reagents, solvents, products) 1.37M lines total from patent literature (USPTO 1976 - 2024) and from academic literature (2.5% total). Data converted from existing USPTO dataset 1] and data generated by parsing by custom design. Data extraction by OSCAR (semantic) or ChatGPT (LLM), molecule identification by OPSIN and custom synonym list. All SMILES are RDKit-safe with duplicate reactions removed. Please note that the data have been collected in an semi-automated process, the dataset is certainly not without errors.More information on https://kmt.vander-lingen.nl.1] Chemical reactions from US patents (1976-Sep2016), Daniel Lowe. Link.

The data extract is a series of compressed ASCII text files of the full data set contained in the Canada Vigilance Adverse Reaction Online Database. It is intended for users who are familiar with database structures and setting up their own queries. Find details on the data structure required for the data file in the Canada Vigilance Adverse Reaction Online Database - Data Structure. In order to use the data, the file must be loaded into an existing database or information system provided by the user. The Canada Vigilance Adverse Reaction Online Database contains information about suspected adverse reactions (also known as side effects) to health products, captured from adverse reaction reports submitted to Health Canada by consumers and health professionals, who submit reports voluntarily, as well as by market authorization holders (manufacturers and distributors), who are required to submit reports according to the Food and Drugs Regulations. Information concerning vaccines used for immunization have only been included in the database since January 1, 2011. Indication data has recently been added to the data extract files and the Detailed Adverse Reaction Report. Indication refers to the particular condition for which a health product was taken. For example, diabetes is an indication for insulin. Health products are often authorised for use in treating more than one indication. Note: The database cannot be used on its own to evaluate a health product's safety profile. It does not provide conclusive information on the safety of health products, and is not a substitute for medical advice. Should you have an issue of medical concern, consult a qualified health professional.

The data of the article "General reactive machine learning potentials for CHON elements"

This dataset consists of rate constants, half-lives and activation energy values for hydrolysis of organic chemicals compiled from journal publications and regulatory reports. The dataset was used to develop a ranked library of transformation reaction schemes for abiotic hydrolysis of organic chemicals under environmentally relevant conditions. The spreadsheet file HydrolysisRateConstants_est6b05412.xlsx contains a compilation of 187 literature-reported hydrolysis half-lives adjusted to pH 5, 7 and 9 and temperature of 25°C. The spreadsheet file HydrolysisActivationEnergy_est6b05412.xlsx contains a compilation of 58 literature-reported activation energies for hydrolysis reaction schemes. This dataset is associated with the following publication: Stevens, C., J. Patel, J. Jones, and E. Weber. Prediction of Hydrolysis Products of Organic Chemicals under Environmental pH Conditions. ENVIRONMENTAL SCIENCE & TECHNOLOGY. American Chemical Society, Washington, DC, USA, 51(9): 5008–5016, (2017).

BIOINF595 W2025 Bioactivity Project Dataset Author: Carl Mauro The reaction data used in this project is from the following publication, accessed through the Open Reaction Database (https://open-reaction-database.org/). The original data is used under an MIT license, and is under copyright by the original authors (see LICENSE.txt file for details). Ahneman, D. T.; Estrada, J. G.; Lin, S.; Dreher, S. D.; Doyle, A. G. Predicting Reaction Performance in C–N Cross-Coupling Using Machine… See the full description on the dataset page: https://huggingface.co/datasets/cmmauro/ORD_Ahneman_2018.

The following information is given for each entry in this database: the reference for the data; the reaction studied; the name of the enzyme used and its Enzyme Commission number; the method of measurement; the conditions of measurement (temperature, pH, ionic strength, and the buffer(s) and cofactor(s) used); the data and an evaluation of it; and, sometimes, commentary on the data and on any corrections which have been applied to it. The absence of a piece of information indicates that it was not found in the paper cited.

Dataset containing reaction centers used to train the disconnection aware model

The MNXref reconciliation of metabolites and biochemical reactions namespace

Abstract Reaction Mechanism Generator (RMG) constructs kinetic models composed of elementary chemical reaction steps using a general understanding of how molecules react. Species thermochemistry is estimated through Benson group additivity and reaction rate coefficients are estimated using a database of known rate rules and reaction templates. At its core, RMG relies on two fundamental data structures: graphs and trees. Graphs are used to represent chemical structures, and trees are used to represent ...

Title of program: RMG Catalogue Id: AEZW_v1_0

Nature of problem Automatic generation of chemical kinetic mechanisms for molecules containing C, H, O, S, and N.

Versions of this program held in the CPC repository in Mendeley Data AEZW_v1_0; RMG; 10.1016/j.cpc.2016.02.013

This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018)

The record contains quantum mechanical (QM) global reaction route map (r-map) data. R-map is chemical reaction pathway networks, which compose equilibrium (EQ) and dissociation channel (DC) and transition state (TS) structures connected via intrinsic reaction coordinates (IRC) obtained by QM calculations. These are contents of RMapDB, which was published first in 2010 as a prototype and has been available online since 2014. The record contains global r-maps of three- to five-atom molecular systems. It contains also a conformational r-map of alpha-D-glucose and a global r-map of C2H4O2, which were discussed in potential energy surface-based conformational analysis and three-dimensional substructure search with the general root mean square deviation (G-RMSD) method. The RMapDB database has been developed in the RMap project for data chemistry based on QM chemical reaction route maps, together with an analytical tool RMapViewer and a server system RMapServer.