Questions tagged [databases]

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14
votes
3answers
1k views

Are there any datasets containing molecules with more than 38 heavy atoms?

I have been testing a machine learning approach for molecular energy prediction. The current dataset that I have is QM9, which is consist of molecules with up to 9 heavy atoms. I was wondering if ...
9
votes
1answer
66 views

What does “reaction rank” in Reaxys stand for?

By exporting some search results from Reaxys, I found "Reaction rank" to be one of the columns in the Excel file. In my file, values descend from 107 to 52 and skip some values in-between too. Does ...
7
votes
2answers
153 views

Open resource for spectroscopic raw data

Is anyone aware of reliable resources (ideally public) which allow the user to download the raw spectroscopic data such as infrared spectrum of small organic molecules, or rotational spectrum of HCl/...
7
votes
1answer
123 views

Validation of _atom_site_frac_*: Range outside of [0,1)?

I have the following cif file ...
7
votes
2answers
1k views

What databases or repositories are there that have generalized SMILES for functional groups?

Does a resource exist that has the SMILES formula of the generalized pattern that represents the group? For instance: I have the aldehydes group, which has the pattern: ...
6
votes
2answers
406 views

What is a good source for large tables on the properties of water?

I'm currently doing an investigation for school on finding the Clausius-Clapeyron relation/gradient for boiling water and comparing it to the gradients along my line of best fit. It is given by the ...
6
votes
1answer
1k views

Finding cubic ice CIF files in crystal database

Could anyone please tell me where I could find the the structure of cubic ice (ice Ic) as a CIF file? I have been searching the cambridge structural database using "H2O", "water", "dihyrogen oxide" ...
5
votes
2answers
2k views

How can I get xyz coordinates of atoms of a unit cell structure from CIF format files?

I'm trying to run DFT or other 1st principle simulation of Pyrope ($\ce{Mg3Al2Si3O12)}$ and Grossular $\ce{(Ca3Al2[SiO4]3)}$ unit cell structure. So, I'm looking for unit cell xyz periodic box ...
5
votes
2answers
63 views

Where can I find ranges of isotope abundances?

I'd like to know how much stable isotopes like $\ce{^{13}C}$, $\ce{^2H}$, $\ce{^{17}O}$ and $\ce{^{18}O}$ deviate from their natural abundances in the earth's crust among all possible compounds we may ...
5
votes
4answers
256 views

What is the best way to convert SMILES strings to file names?

I would like to convert SMILES strings into file names. There are many characters to avoid in file names, i.e. \/:*?"<>| or maybe even ...
5
votes
1answer
285 views

Chemical time scales

In calculating UV/VIS spectra with computational procedures (say, TD-DFT), it is commonly assumed that the geometry of the ground-state is still valid also for the excited state due to the short time ...
5
votes
2answers
669 views

What is the correct regular expression for InChI?

When I look for a regular expression for InChI, I succeed on EBI's MIRIAM Registery website: ...
5
votes
1answer
150 views

Algorithm used by PubChem to determine the 2D layout assignment for Compound entries?

The PubChem database provides 2D structures for entries in its Compounds database: ftp://ftp.ncbi.nlm.nih.gov/pubchem/Compound/ (ftp link to download examples) On the page linked below, under the "...
5
votes
0answers
230 views

Pseudo 3D skeletal structure style which emphasizes geometry

If one searches and navigates to a wiki page for, say, dichlorodifluoromethane one sees the 2D skeletal structure of the compound as below This representation appears to be of a particular style that ...
4
votes
1answer
1k views

Is there an open Chemical database that includes GHS/CLP classifications?

I'm looking for a Chemical database that is up to date (via a firm, experts or crowdsourcing) is open and free to use (best via an API) contains the CLP/GHS classifications for chemicals I have not ...
3
votes
1answer
119 views

Energy cost of C−N rotation in hydroxamate group

I am looking for a literature reference on the energetic cost of C−N rotation in hydroxamate group such in LC5 in water. I have been googling for a while.
3
votes
1answer
2k views

Free chemical reactions database

I'm creating a program, which predicts reactions of compound. So, I need a database of chemical reactions. And I need both inorganic and organic reactions. But I can't use Scifinder or Reaxys because ...
3
votes
1answer
251 views

Where can I find example MS, IR, NMR spectra for teaching molecular spectroscopy?

I am teaching a course on analytical chemistry, and I would like to give my students MS, IR and NMR spectra to practice with. It would be ideal if they could analyze spectra in a more "realistic" way ...
3
votes
0answers
18 views

Any large databases of IR Spectra that you are able to download many spectra in bulk [closed]

I am currently working on a machine learning project, in which I need access to many IR spectra, the more the better, in order to build a classifier that will used some unsupervised learning in order ...
3
votes
0answers
42 views

Unique identifier for chemical substances?

One famous database for chemical substances is PubChem. If one reads the section about other identifiers than the PubChem ID for Ethanol one gets several CAS numbers (potentially deprecated ones as ...
3
votes
0answers
85 views

Which organic compounds have the most strongly negative enthalpies of formation?

I've been using the NIST Webbook to list organic compounds and look at their heats of formation (kJ/g, not mol). If I limit myself to three carbons, I still get over 400 results. I can use some ...
3
votes
0answers
556 views

Calculating Surface Area of Compound

Is there any way to calculate the surface area of compounds such as 2,5-dimethylhexane or 3-methylpentane? If not, is there a database that has information on surface area of these compounds (not ...
2
votes
2answers
79 views

What are the GDB-13 criteria for “synthetically accessible organic molecules”?

I'm trying to understand the QM datasets (QM7, QM8, QM9), however, in the description of QM7 the data is described as follows: [The] QM7 dataset, which is a subset of GDB-13 (a database of nearly 1 ...
2
votes
1answer
50 views

Is there any book where specific heat capacities are given?

I want to find the value of the specific heat capacity of aluminium nitrate nonahydrate, in order to calculate mixing effects in a chemical reaction. I am looking for a source, such as a book or link ...
2
votes
1answer
118 views

Help on alternative terpene names and naming schemes

I am a software developer and currently parsing data involving terpene profiles of plant samples. The data in question uses different ways of naming the same terpenes in-between samples and since this ...
2
votes
3answers
84 views

Does anyone know a database that shows the effect of electrolyte concentration on the production of hydrogen gas during electrolysis of water?

I'm currently studying in the International Baccalaureate model. This high school model asks their students to do an individual work called the Internal Assessment. One of the subjects I study is ...
2
votes
1answer
190 views

Need help interpreting this data table (provided below)

I am confused about this data table. Can someone please explain how this person got a linear alkanes of differing molar masses? (I know some basics of organic chemistry, but I'm still learning.) Are ...
2
votes
0answers
146 views

Spectral database in the UV-Vis/NIR and IR regime

I'm searching for a bunch of spectra (some tens), preferably with intense bands in the Vis spectrum, to play around with (calculating chromaticity, etc.). They should range from 250 nm to 2500 nm (UV-...
1
vote
1answer
182 views

What is the meaning of the phase state label (cr,l) appearing in ATcT thermochemical data tables?

I was examining data associated with this post on the heat of solution of ammonium nitrate when I came upon the NIST ATcT data page which lists the heat of formation of $\ce{(NH4)NO3(cr,l)}$. In this ...
1
vote
0answers
26 views

API or database for verifying chemical reactions [closed]

Is there a database or API(rest calls) for verifying chemical equations? Example, Na + Cl -> NaCl + Loss of energy. So if I want to verify if there is a loss of energy or gain of energy? Is there ...
1
vote
0answers
14 views

Find drugs that have a particular solvent in a database [closed]

Is there a database where I can filter drugs for animal/human use by what ingredients/solvents they have? I'm specifically looking for all the drugs with a specific solvent/chemical compound.
1
vote
0answers
33 views

Online list of water of crystallisation?

I was extremely happy to recently receive a copy of the Nuffield Revised Book of Data but was somewhat disappointed to find that it did not list data on the water of crystallisation for various ...
1
vote
0answers
89 views

Where can I find a downloadable database of basic physical and chemical properties?

The web has many online databases of properties of compounds locked behind search interfaces, but I can't find anything you can actually download. I want a corpus of data that might allow me to, say, ...
1
vote
0answers
27 views

Deliquescence database

I am looking for a database or printed document providing the RH0 (relative humidity above which deliquescence will occur) for inorganic salts. I've looked everywhere on the internet can find nothing.
0
votes
2answers
171 views

How to find chemical market value [closed]

I would like to retrieve pricing information for specific chemicals. Is there a centralized resource for this? Edit: I want to clarify that this type of data is to conduct a techno-economic study. I ...
0
votes
1answer
503 views

Molar absorption coefficient of H2SO4(aq) for UV-vis spectrophotometry

I am wondering if there is anything in the literature that can tell me what is the molar absorptivity (i.e. molar extinction coefficient) of aqueous sulfuric acid at a given wavelength (in my case, I ...
0
votes
1answer
410 views

Where can I find reliable data for melting points of organic compounds?

I'm interested in the melting/freezing points of organic compounds, but the online literature has data that's all over the map. I can understand that especially for isomers of alkanes, pure samples ...
0
votes
1answer
154 views

What is the difference between ΔfH and H-H° in NIST–JANAF tables?

Can someone explain the difference between $Δ_\mathrm{f}H$ and $H-H^\circ$ in NIST–JANAF tables?
0
votes
1answer
376 views

where can I find experimental compressibility factor values?

I am interested in experimental compressibility factors for various gases, such as methane and carbon monoxide. Not only for standard pressures and room temperature, but in a range from 1 to a few ...
0
votes
1answer
49 views

Database for experimental diatomic ionization energies

I am looking for a database, in which the experimental ionization energies (and e.g. heat of formation) of atoms and diatomic molecules are listed as files. If it comes with a Python package, that ...
0
votes
1answer
52 views

Are there any fluorophores with lifetimes in the micro to milli second range?

I'm looking for a fluorophore with exceptionally long lifetime to use in an oxygen optode (the longer the lifetime the less timing precision needed in the electronics). So far the longest I have ...
0
votes
0answers
22 views

Do any decent thermochemical databases exist? [duplicate]

The more thermochemical properties the better, but specific heat/ specific heat capacity is what I am looking for.
0
votes
0answers
75 views

Looking for experimental data for titration curves

I am looking for real, open source and free experimental dataset (not image, scan of table) of acid/base titration curves: pH versus titrant volume for many combination (strong/weak acid/base, ...
0
votes
0answers
111 views

Experimental bond lengths and binding energies of diatomic molecules

Is it possible to find the experimental values of the bond length and the binding energy of the diatomic molecules $\text H_2$, $\text{Be}_2$, and $\text{Ar}_2$ in one source? I found a lot of ...
-1
votes
0answers
22 views

What are the signs in `_atom_site_label` in a CIF file mean?

I am trying to write a program that will be able to read CIF files. I am testing on a CIF file like this: ...