The given is the original CT data for Sample #1 and Sample #2 which supports the findings in the paper "Changes in reaction surface during the methane hydrate dissociation and its implications for hydrate production".

This dissertation seeks to resolve how step edges at a platinum surface influences reaction probabilities. Additionally, steps are made to develop a setup to vibrationally excite CO2 in a supersonic molecular beam. The data comprises mainly of mass spectrometric data and LEED images. The full lab journals are included. The data are placed in folders that are labelled by their date.

The data underlying this published work have been made publicly available in this repository as part of the IMASC Data Management Plan. This work was supported as part of the Integrated Mesoscale Architectures for Sustainable Catalysis (IMASC), an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Basic Energy Sciences under Award # DE-SC0012573.

This dataset contains information on each of the 14 reactions used in the paper, the geometries for these reactions, the product of the quantum reaction rate constant and canonical reactant partition function and the flux-flux correlation function time series values for each reaction-temperature combination.

reaction_details.csv

This is a .csv file containing additional details on the reactions used in this paper. Each row contains one reaction/temperature combination, of which there are 55.

Column descriptions:

reaction_number: Reaction identifier number used in this work

reaction: The chemical reaction equation

metal_surface: atomic symbol of metal surface

facet_number: Miller indices of surface

reactants: Python dictionary object of reactants and their quantities

products: Python dictionary object of products and their quantities

reaction_energy [eV]: reaction energy in electron-volts

activation_energy [eV]: activation energy of reaction in electron-volts

temperature [K]: The randomly assigned temperature a calculation was run for

kQ_Cff [1/au]: The calculated integrated reaction rate product at corresponding temperature {1,2,3,4} in units 1/(au time).

reaction_split: Train/test placement of that reaction/temperature combination for reaction split

temperature_split: Trian/test placement of that reaction/temperature combination for temperature split

catalysishub_reactionID: Catalysis Hub reaction ID identifier for referencing catalysis hub database

doi: digital object identifier of original publication for which DFT calculations were performed

Flux_flux_correlation_functions:

Directory containing flux-flux correlation function time series values for each reaction temperature combination. Values are organized in subdirectories, one for each of the 14 reaction. In each subdirectory .csv files are labeled by reaction number and temperature in Kelvin. Each csv file contains a column with time points [au of time] and the corresponding flux-flux correlation function value in units [1/(au of time)2].

Geometries:

Directory containing geometry files for each reaction. Geometries of reactants on the surface were shifted respect to those supplied by catalysis hub to create continuous reaction pathways where necessary. Geometry files are organized in subdirectories for each reaction. When complete nudged elastic band (NEB) minimum energy paths (MEP) were not available ,subdirectories contain a products.xyz, reactants.xyz, and TSstar.xyz file (reactions 1 to 11) otherwise the complete set of NEB MEP images labeled neb{n}.xyz is given (reactions 12, 13, 14).

Metadata for the open access publication "How the anisotropy of surface oxide formation influences the transient activity of a surface reaction" (https://doi.org/10.1038/s41467-020-20377-9) A complete list of dataset files can be seen in "filelist.txt". The files contain the data that generated the figures in the referenced publication and are structured according their order of appearence in the publication. The dataset contains the following file types: standart image files (bmp, tif) SPEM spectroscopy data (hdf, tsf) PEEM video data (his, ROI) QMS mass spectrometry data (SI-d) Additional context, methodology, and technical details is provided in the publication and its supporting information.

A proper representation of chemical kinetics is vital to understanding, modeling, and optimizing many important chemical processes. In liquid and surface phases, where diffusion is slow, the rate at which the reactants diffuse together limits the overall rate of many elementary reactions. Commonly, the textbook Smoluchowski theory is utilized to estimate effective rate coefficients in the liquid phase. On surfaces, modelers commonly resort to much more complex and expensive Kinetic Monte Carlo (KMC) simulations. Here, we extend the Smoluchowski model to allow the diffusing species to undergo chemical reactions and derive analytical formulas for the diffusion-limited rate coefficients for 3D, 2D, and 2D/3D interface cases. With these equations, we are able to demonstrate that when species react faster than they diffuse they can react orders of magnitude faster than predicted by Smoluchowski theory, through what we term “the reactive transport effect”. We validate the derived steady-state equations against particle Monte Carlo (PMC) simulations, KMC simulations, and non-steady-state solutions. Furthermore, using PMC and KMC simulations, we propose corrections that agree with all limits and the computed data for the 2D and 2D/3D interface steady-state equations, accounting for unique limitations in the associated derived equations. Additionally, we derive equations to handle couplings between diffusion-limited rate coefficients in reaction networks. We believe these equations should make it possible to run much more accurate mean-field simulations of liquids, surfaces, and liquid–surface interfaces accounting for diffusion limitations and the reactive transport effect.

We report here reactive dynamics (RD) simulations of the adsorption and decomposition of a gas of 20−120 methane, ethyne, ethene, benzene, cyclohexane, or propene molecules interacting with a 21 Å diameter nickel nanoparticle (468 atoms). These RD simulations use the recently developed ReaxFF reactive force field to describe decomposition, reactivity, and desorption of hydrocarbons as they interact with nickel surfaces. We carried out 100 ps of RD as the temperature is ramped at a constant rate from 500 to 2500 K (temperature programmed reactions). We find that all four unsaturated hydrocarbon species chemisorb to the catalyst particle with essentially no activation energy (attaching to the surface through π electrons) and then proceed to decompose by breaking C−H bonds to form partially dehydrogenated species prior to decomposition to lower order hydrocarbons. The eventual breaking of C−C bonds usually involves a surface Ni atom inserting into the C−C bond to produce an atomic C that simultaneously with C−C cleavage moves into the subsurface layer of the particle. The greater stability of this subsurface atomic C (forming up to four Ni−C bonds) over adatom C on the particle surface (forming at most three Ni−C bonds) is critical for favorable cleaving of C−C bonds. For the two saturated hydrocarbon species (methane and cyclohexane), we observe an activation energy associated with dissociative chemisorption. These results are consistent with available experimental reactivity data and quantum mechanics (QM) energy surfaces, validating the accuracy of ReaxFF for studying hydrocarbon decomposition on nickel clusters.

This Zip file contains the cartesian coordinates of optimized stationary points of the O(³P, ¹D) + HCCCN(X¹Σ⁺) potential energy surface published in our article “Reactions O(³P, ¹D) + HCCCN(X¹Σ⁺) (Cyanoacetylene): Crossed-Beam and Theoretical Studies and Implications for the Chemistry of Extraterrestrial Environments” (J. Phys. Chem. A 2023, 127, 3, 685–703), that can be found in https://doi.org/10.1021/acs.jpca.2c07708.

All calculations have been performed with Gaussian 09, Revision D.01.

All structures have been optimized at B3LYP/aug-cc-pVTZ level of theory.

Counts and relative abundances of marker genes from total archaea, bacteria, and fungi observed by qPCR in surface water microbial communities

This event has been computationally inferred from an event that has been demonstrated in another species.

The inference is based on the homology mapping from PANTHER. Briefly, reactions for which all involved PhysicalEntities (in input, output and catalyst) have a mapped orthologue/paralogue (for complexes at least 75% of components must have a mapping) are inferred to the other species. High level events are also inferred for these events to allow for easier navigation.

More details and caveats of the event inference in Reactome. For details on PANTHER see also: http://www.pantherdb.org/about.jsp

Tuning the electrode surfaces for better bubble management is a promising approach to increase the efficiency of alkaline water electrolysis. Therefore, Direct Laser Writing was used to structure Nickel electrodes with a dual wetting surface. The applied pillar-like structure combines superhydrophilic behavior and strong spreading of the liquid across the electrode with hydrophobic bubble nucleation sites. In addition, the electrochemically active surface area is increased by a factor of 9. As a result, the overpotential has been significantly reduced, while the size of the detached bubble has increased. The present data set compares three different electrodes, a non-structured reference electrode and two laser structured electrodes with different depths of the structure, at applied current densities of j = -20, -50 and -100 mA/cm² in terms of electrode potential, detached bubble size and number of nucleation sites. As electrolyte 1 M KOH was used. All experiments were carried out under ambient conditions (T = 293 K,p = 1 bar).

Description of Data.zip:

An overview of all performed experiments is given in the file Summary.csv. The data is analyzed as described in the corresponding journal publication Dual wetting electrode surfaces for alkaline water electrolysis. Each data set is stored in a .hdf5-file, with the relevant metadata incorporated into the attributes assigned to the groups/datasets within the .hdf5-file. The data files are structured in groups as follows:

• Electrochemical Measurement Data
  • Galvanostatic Measurement Data
  • CV double-layer capacitance
  • LSV onset potential
• Results
  • Detected Bubbles Sideview
• Sideview Raw Images (only for SH2_LS_Pil_01.hdf5)

With the exception of a single comprehensive data set comprising unprocessed images (SH2_LS_Pil_01.hdf5), the remaining raw images from all performed measurements can be made available upon request.

This study explores the synergy between photocatalytic oxidation and membrane filtration using a photocatalytic membrane. Titanium dioxide coated alumina membranes were fabricated and tested in a customized Photocatalytic Membrane Reactor (PMR) module. The discoloration of methylene blue (MB), 3.2 mg.L^-1 in an aqueous solution, was evaluated in dead-end filtration mode. A simple 1D analytic transport and surface reaction model was used based on advection and diffusion, containing intrinsic retention by the membrane and reaction kinetics to predict the permeate concentration. The discoloration of MB by the photocatalytic membrane could be well described by a single retention and reaction rate constant (second Damköhler number) for fluxes from 1.6 to 16.2 L.m^-2.h^-1. The model furthermore indicates the potential synergy between membrane retention, which leads to increased concentration, and accompanying photocatalytic conversion, at the membrane surface.

Data and scripts for the preprint "Automatic Mechanism Generation Involving Kinetics of Surface Reactions with Bidentate Adsorbates".

Lewis acid sites (LAS) at the CHA(001) and CHA(101) surfaces are investigated regarding their activity for MeOH-mediated hydrogen transfer reactions from MeOH to alkenes, yielding alkanes and formaldehyde. Direct MeOH decomposition to formaldehyde and hydrogen is also investigated. Furthermore, the coupling of the produced olefins with formaldehyde to dienes and H2O via the Prins reaction is studied. The reactivity of LAS for these reactions is compared to that of bulk Brønsted acid sites (BAS) and surface BAS. Periodic density functional theory (DFT) is used in connection with DLPNO-CCSD(T) calculations on cluster models. Hydrogen transfer reactions are found to be often more favorable on LAS, while both LAS and BAS have similar activity for Prins reactions.

This repository houses electronic structure data and metadata generated as part of a computational chemistry case study, enabling full analysis of the paper "WhereWulff: A semi-autonomous workflow for systematic catalyst surface reactivity under reaction conditions" by Rohan Yuri Sanspeur, Javier Heras-Domingo, John R. Kitchin and Zachary Ulissi.

Challenges in quantifying how force affects bond formation have hindered the widespread adoption of mechanochemistry. Here, parallel tip-based methods are used to determine reaction rates, activation energies, and activation volumes of force-accelerated [4+2] Diels-Alder cycloadditions between surface-immobilized anthracene and four dienophiles that differ in electronic and steric demand. The rate dependences on pressure are unexpectedly strong, and significant differences are observed between the dienophiles. Multiscale modeling demonstrates that, in proximity to a surface, mechanochemical trajectories ensue that are distinct from those observed solvothermally or under hydrostatic pressure. These results provide a  framework for anticipating how experimental geometry, molecular confinement, and directed force contribute to mechanochemical kinetics.

Collective variables (CVs) are crucial parameters in enhanced sampling calculations and strongly impact the quality of the obtained free energy surface. However, many existing CVs are unique to and dependent on the system they are constructed with, making the developed CV non-transferable to other systems. Herein, we develop a non-instructor-led deep autoencoder neural network (DAENN) for discovering general-purpose CVs. The DAENN is used to train a model by learning molecular representations upon unbiased trajectories that contain only the reactant conformers. The prior knowledge of nonconstraint reactants coupled with the here-introduced topology variable and loss-like penalty function are only required to make the biasing method able to expand its configurational (phase) space to unexplored energy basins. Our developed autoencoder is efficient and relatively inexpensive to use in terms of a priori knowledge, enabling one to automatically search for hidden CVs of the reaction of interest.

Spectroscopic parameters of the dye-labeled B7 probes and respective complexes with AV and SAV.

Reaction energies and atomic structures from first-principles electronic structure calculations.

In this record we provide the data to support our recent finding on surface catalyzed cycloaromatization. Immobilization of organic building blocks on metal surfaces and their coupling via thermally induced C-C bond formations are developing as an important addition to the toolbox of organic and polymer synthesis. Additional advantages of this technique are the in situ monitoring of the reaction by scanning probe methods and the accessibility of insoluble and reactive carbon nanostructures. The diversity of conceivable products, however, sensitively depends on the number of available on-surface reactions. In the manuscript where the results are discussed, we introduce an unprecedented example, the intermolecular oxidative coupling of isopropyl substituents of arenes. With a new phenylene ring being formed, this [3+3] dimerization can be regarded as a formal cycloaromatization. The synthetic value of this novel reaction is proven by the synthesis of polyarylenes and co-polyarylenes, which we demonstrate by synthesizing poly(2,7-pyrenylene-1,4-phenylene). Scanning tunneling microscopy and non-contact atomic force microscopy studies complemented by density functional theory calculations are employed to obtain mechanistic insights into the title reaction.