Questions tagged [databases]
For questions about finding and using databases of material and molecular properties.
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Which one of the following showing the correct structure Jsmol or Vesta? Or they are just same
Let me explain. I found that the structure for TiFeSi given in the ICSD database using Jsmol software is a little different from what can be obtained using Vesta software using the same cif file ...
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Source for Hammett Parameters useable in QSAR model training?
I tried to create a QSAR (Quantitative Structure Activity Relationship) model for my thesis that tries to predict the melting points of certain ZIFs (Zeolitic Imidazolate Frameworks) based on relative ...
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How to calculate pharmacore features?
Cross-posted at Bioinformatics.SE.
I want to use the enzyme ß-Glucuronidase with the pharmit database. I uploaded my file for the receptor from pdb file. How can I get the pharmacore features? So one ...
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Database on calculated molecular vibrations including coordination complexes?
Related to the question Are there dashboards displaying experimental properties of molecular materials?
My question is: Are there any good, free, online databases on calculated vibrational modes of ...
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Why are some point groups for single atoms listed as Oh in the CCCBDB?
Does anyone know why the CCCBDB database lists the tin cation and antimony atom as having the Oh point group (please see the screenshot below from CCCBDB when I look at "All molecules sorted by ...
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Trouble finding pdfs of "Tables of Interatomic Distances and Configuration in Molecules and Ions" series books
I am currently trying to find molecular geometry data prior to 1960, and it seems like
"Tables of Interatomic Distances and Configuration in Molecules and Ions (1958). Special publication No. 11. ...
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Software for storing information of large number of atomic structures into database file
Say I have a MD trajectory that contains a million snapshots (i.e. a million atomic structures). Each snapshot contains some calculated information (either by DFT or some force field) such as energy, ...
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How to query 2D materials on materials project?
I would like to use the materials project API to search materials with some properties but to restrict my search only to two-dimensional materials.
How to do it?
Web-pages for materials contain the '...
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Database (or table) of functions obeying symmetry properties of space groups
I'm looking for a table or database containing mathematical functions that belong to crystallographic space groups by having the same symmetry elements.
Imagine a 2D square planar lattice. It has a 4-...
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What would be the preferred format for a geometry database?
Introduction (analogy to basis set database files)
Many programs have a database of basis sets stored in a file such as the following (so that users can just specify in their input file something like ...
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Is there a method or web API to get pricing from a SMILES string?
A variety of databases include "purchasability" (e.g., ZINC) and can be filtered as such. Or you can download just the purchasable compounds.
I'm curious if there are methods or web APIs to ...
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Which Python packages, APIs or online databases may be used for a Python script to find bond dissociation energy between two arbitrary atoms?
Let us say that I wish to create a function that may do the following:
>>> find_bond_energy(atom1="C", atom2="O", order=3)
1072 kJ/mol
...
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What is the bond length of O2--?
I need the bond length in Å for $\ce{O_2^{--}}$ from this geometry database page (type "O2--" for the input).
I get a bunch of possible values. I don't know much about those yet but after ...
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Best resources for someone going from experimental to computational chemistry
In a few months, I will complete my PhD and I'm considering leaving experimental chemistry and looking for a postdoc on computational chemistry. During my PhD I used some computational tools like ...
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List of properties of molecules categorized by the number of atoms?
Is there an online database having information on molecules with a certain number of atoms? For example, properties of tri-atomic molecules?
There is this table that I got from NIST which gives a few, ...
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Pharmaceutical solubility databases?
I am looking for databases for the solubility of pharmaceuticals (small drug molecules up to 1500 g/mol MW) in a variety of pure and mixed solvents.
There is the Handbook of solubility data for ...
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Repository of Common Surfaces
Are there any repositories of crystal surfaces? Due to orientation / termination of surfaces, occasionally it is non-trivial to decide how exactly to cut a surface for things such as oxides. I ...
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1T phase MoS2 CIF File
The peak shift for XRD of the 1T and 2H phases of $\ce{MoS2}$ differs by a few degrees (just below 10 degrees for 1T, 14 degrees for 2H).
In Rietveld Refinement, a standard CIF file can be used for ...
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Database of surface electronic structure [closed]
I'd like to compare my simulation result of a TiO2-110 surface's electronic structure, but all the literature shows too many different results, so I'd like to look for a database for surface ...
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How to alter the charge and multiplicity of a molecule in Gaussian?
I want to perform redox potential calculations using the Gaussian. To check if I'm setting things up correctly, I want to compare it to a benchmark database published by Grimme et al.[1] I performed ...
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Is there a benchmark paper that takes into account how often each molecule is studied?
There are many benchmark sets in different branches of computational chemistry and physics, that are frequently used to assess the "average error" of a method for a certain property, on a ...
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Citing a pseudopotential
I conduct my DFT calculations using the SIESTA DFT package. For this, I obtained the pseudopotentials from this site which says that they have obtained the data from the Abinit database. However I do ...
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The format and values provided by Basis Set Exchange
In this question and answers, I found that Basis Set Exchange provides information about the orbitals (e.g., the orbital exponents and contraction coefficients). For example, the following example is ...
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How can I find the parameters in a basis set?
I have a question about the basis functions of Gaussian. When the basis function is set (e.g., 6-31G), I would like to know the specific value of Gaussian's parameters for each atom.
In particular, I ...
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ASE convesion of Trajectory file to XDATCAR
The issue here is while converting a TRAJ file to POSCAR, it works. But, for TRAJ to XDATCAR, it shows TypeError: images should be a sequence of Atoms objects. (...
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Simple code for polarizable force-field molecular dynamics? [closed]
I am interested in writing my own molecular dynamics code that uses a polarizable force-field. I am wondering if there are relatively simple "toy repositories" for these models such as is ...
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Is there a site to obtain or create membranes?
I am interested in creating an enterocyte intestinal basal membrane.
So, I wonder if there is a database or site where the membrane could be downloaded or created.
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Best way to read forces and positions and energies into Atomic Simulation Environment (ASE)?
My current procedure is to create a .xyz file out of my MD run for a crystal structure. I can read the energy and also each atomic position. But I want to add forces. If I add forces as the additional ...
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Functional group detection for group contribution methods
I would like to be able to parse a molecule into its functional groups, and, also, know the number of occurrences of each.
A similar question was asked on matter modelling specifically for xyz files. ...
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Large dataset with conductivities of materials and chemical compounds? [closed]
I'm looking for a fairly large (>100k) dataset of chemical compounds (and materials) that has conductivities. I've looked at PubMed, but couldn't find conductivities.
I would ideally like to avoid ...
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What are good protocols for creating a database based on python? [closed]
I am aware of software tools such as atomate, but that is quite specific to crystals. There are other equally specific workflows - I think we all have our own...
What I am interested in is making my ...
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Pycalphad "Failed while parsing" Yttrium from light alloys database
The code in question is just 2 lines used to import the "COST507 database for light alloys" (downloaded from the opencalphad homepage http://www.opencalphad.com/).
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Is there a database where one can find the Electron Density data of materials?
The database I am looking for may be experimental, computational or user-generated data. If I end up using the data, I will be providing the necessary citations and credits. Thank You.
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What are the databases of semiconductor properties?
Is there any database listing the experimentally-determined properties of semiconductor materials - things like Band Gap and Electron Mobility. These are easily found for common materials like ...
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Are there dashboards displaying experimental properties of molecular materials?
A dataset is generally a collection of data.
A database is an organized collection of data, allowing different kinds of queries.
A dashboard is a graphical user interface that is employed to make ...
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Is there a free online repository where I can download X-ray diffraction (XRD) data?
It's as the title of the question states. To be specific, I'm wondering if there are any free online repositories where I can download (.csv or .txt. or .xsl) files for x-ray diffraction (XRD) data.
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Finding parameters for a molecule in various forcefields
Let's say I want to run a simulation for benzene in GROMACS using parameters from a certain force-field. I logged on to the Automated Topology Builder, I looked up benzene, and I found an ITP file for ...
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Where did the "Computational Chemistry Comparison and Benchmark DataBase" find its scaling factors for vibrational specra?
I worked with gaussian to simulate vibrational IR and Raman spectra. For that purpose, I scaled the vibrational frequencies from my gaussian calculation with the scaling factors from this website:
...
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Band structure and density of states disagreement (mp-19092)
My question is both specific and general. While looking through the materials project database I found this entry. The band structure reported and density of states are dramatically different it ...
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Interpret 2D and 3D data from a PubChem summary of organometallic molecule? Can I "flatten" it when showing on a surface?
I need to "build" an organometallic molecule in Blender/Python then represent it resting on a crystal surface.
I'm looking at a PubChem summary for Chloroaluminum phthalocyanine and I can ...
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Reliability about the predicted two-dimensional crystal structures based on DFT high-throughput calculation?
Computational 2D Materials Database (C2DB), 2D structures and layered materials, and 2D Materials Encyclopedia are three major databases for two-dimensional materials based on DFT calculation.
However,...
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Is there a list of all functionals?
A quick google search of the Minnesota Functionals will lead you to the wikipedia page on them where it will state the following:
...
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Alanine dipeptide trajectories dataset
I was looking for a dataset of alanine dipeptide trajectories. I was wondering whether there is such dataset available or it is unlikely to find one and I should start running molecular dynamics ...
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Is there a set of updated, comprehensive benchmarks for speed comparison between different quantum chemistry packages?
I've found a page dedicated to quantum chemistry packages benchmarks, on GitHub, qmspeedtest. But most results there are several years old, and so probably outdated. Is there some place where we can ...
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What software is needed in chemoinformatics or materials modeling, that a solo programmer could work on?
I want to make a pet project in cheminformatics and I need to hear from the community about the actual challenges in chemistry that might be resolved with a digital solution.
I've been working in ...
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Database or repository with values for the Hubbard potential U?
The Materials Project and other materials databases have a nice periodic table on their home page that allows you to search for compounds. For some materials, they give an empirical $U$ value used to ...
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Is there any complete list of open source hubs specifically designed for materials modeling and computational materials science?
Several years ago, I became familiar with nanoHUB for accessing open-source codes and software specifically for computational materials science at the nano-scale as well as PFHub that gives you access ...
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What are some servers that are able to host and share our research data?
Now a days, due to some publish-or-perish politics that gives place to many cases of plagiarism and fake data/results, some journals are asking to submit (and share) the data used in the research. In ...
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Is there a list of all universality classes for phase transitions with examples of each?
I've often had this problem: I have a model that has a phase transition in it, but I don't know what universality class it falls into or what the universality class is called.
Is there anywhere on ...
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Is there a database where we can find previously determined geometries of materials?
For small molecules, NIST has a database of experimentally determined geometries here, and ab initio geometries here. I wonder if there is something similar for materials?