In a recent blog post we were asked to CLOSE the ChemSpider site based on a judgment made around our handling of calcium carbonate. The following comments were made regarding the fact that a logP value was calculated for Calcium Carbonate inside the ChemSpider database. Specifically:

 Here is  the entry 

Chemical Structure CCaO3

Molecular Weight 62.02

logP -0.809

hydrogen bond donors 2

Well, they got the chemical formula right. Calcium carbonate is marble, limestone, chalk. It’s hard and does not dissolve in water. You calculate its molecular weight as follows:

Ca=40 + C=12 + 3 (O=16)

and your child will tell you that it comes to 100. (I’ve missed the decimal point). The monkeys only get to 62 before they give up. I have no idea how they get this. The monkeys also tell us how many hydrogen atoms can be used to bind to other molecules. I can’t see any hydrogen atoms, nor can you but the monkeys found 2.

In a later blog  the comments included:

There are several broken parts.

1) for CaCO3 the system created H2CO3 and calculated that

2) What is the point of calculating logP for a sodium Ion?

3) there is no point in calculating logP for calcium carbonate. It’s insoluble in water and octanol

In our world of “Please Provide Feedback” as requested on this beta site this information would have been great to receive via the Feedback link on the ChemSpider pages. We receive lots of daily feedback…some of it celebratory in nature: Thanks! Cool! Tried it.worked great! The majority of it is constructive in nature.  Some is highly critical – “You don’t have structure X on your database..what type of service is that!”  BUT..I’m not aware of a resource having every structure.

The blog posting was brought to my attention by a ChemSpider user. So, a blogged response here seems appropriate.

1) The Molecular Weight of CCaO3 is, indeed, NOT 62. That’s the molecular weight of the doubly protonated carbonate ion. Known bug – listed on our bug page. It also states on the prediction page now some of the properties presented are calculated for the main component only”. The algorithms calculate the weight for the “primary ion” that we use to feed the LogP prediction algorithm engine. Known bug and it has been fixed. Now we need to recalculate for 10 million compounds.

2) Calcium carbonate certainly does exist in various forms as listed. But it IS soluble. The measured solubility of CaCO3 is 1mg/100 mL. Ask anyone who lives in a limestone area if calcium carbonate is soluble. . Boil a kettle dry and see what deposits on the element. Cut a copper pipe open and check for the furring from hard water. Check out wikipedia  details about solubility. It might not be highly soluble but many compounds can be highly insoluble but still have a measured octanol-water partition coefficient. But I do get the point.it’s not what you would call an organic molecule so why calculate a logP value?

3) The number of hydrogen bond donors is two. Ah-ha. Now the meat of the problem. There are three issues here really.1) it is not easy to communicate the details of all prediction algorithms before people click a button (and most people don’t care anyways), 2) We need to continue to expand the FAQ list for such issues and 3) The provider of the algorithm for logP prediction needs to consider whether they would want to change what they report for ions such as carbonate or not. Based on feedback the answer is it’s fine as is.

To explain, when carbonate is dissolved in water it protonates. logP is the partition of any species between 2 solvents, specifically logP generally refers to octanol-water partitioning. So for carbonate ion there would be 3 logP’s (CO3–, HCO3-, H2CO3) in competition, to account for that overall distribution of species.

 Calciium Carbonate Species

Carbonate ion, under the measurement conditions of octanol-water partitioning, likely does actually partition. It may exist in the literature as as an experimental value. I don’t know. However, I think it is valid to list predicted values. I can find such predicted values in the International Safety Cards for the National Institute of Occupational Safety and Health for other carbonates (Barium Carbonate, there are no predicted values for calcium carbonate but it does say it is insoluble and we already know that isn’t true!).

The number of hydrogen donors is the sum of OHs and NHs. One of the forms of carbonate in the multi-species is the doubly protonated form and the number of hydrogen bond donors is actually two.

Clearly, logP is not so simple as everyone thinks! In fact an industry has been built around logP algorithms while the fact is that there has been an increasing shift to logD as the parameter of choice, especially for the pharmaceutical scientists. Why? The majority of compounds are not neutral in the body and they experience different pHs as they migrate through the system. While logP is a very important parameter in many ways it is now overshadowed by logD as an important parameter. ACD/Labs provided ChemSpider with their ACD/LogP batch product as part of our collaboration. They also provide a free add-in for the Freeware ChemSketch package to allow anyone to download and predict logP values. ACD/LogD is their tool providing logD calculations.

As commented by PMR, “I cannot let garbage science go uncommented. That is what peer-review is about. And it can be painful.”

Indeed. It was painful to get the criticism this way…we’d prefer the Leave Feedback since it is beta. However, it appears that prediction is valid. So it’s listed. That said, we welcome feedback from the community about whether to remove this value from the database. Or, simply curate the data yourself!

Stumble it!

7 Responses to “Monkeys and Calcium Carbonate. Should ChemZoo Close its Gates?”

  1. Egon Willighagen says:

    A comment on the beta state. In software development, where the term ‘beta’ possibly comes from, beta means software which has been carefully checked by the authors, fullfills as many quality assurance testing as possible, has no known bugs, or minor at most. Getting the MW wrong for every salt is scary… that sounds more like something in the alpha phase, which is more like a developers release and under developer testing.

    Anyway, I highly recommend currently removing all salts from the visible database until the problems with salts are fixed. Especially for websites it does not hold that ‘any advertisement is good advertisement’.

    PS. blog add the Chemical blogspace.

  2. ChemSpider Blog » Blog Archive » Calcium Carbonate, logP predictions and Chris Lipinski says:

    [...] ChemSpider Blog Just another WordPress weblog « Monkeys and Calcium Carbonate. Should ChemZoo Close its Gates? [...]

  3. Antony Williams says:

    Egon, Thanks for the feedback. We had over 30 people testing the alpha version before we went live. Unfortunately the bias for all of us was on the challenging situations and with a clear bias to pharmaceutical type molecules. VERY unlikely that anyone ever searched a simply salt. Big lesson there…simplicity over complexity.

    That said we will be leaving it at beta since we are 40% of the way through recalculating properties (4.3 million compounds) and will publish all newly calculated properties to resolve the multicomponent issue by end of week we hope (assuming no system failures). At that point issues with alpha/beta declarations are resolved for both you and PMR I believe. Any other issues to report? We welcome all feedback and encourage further responses! Thanks very much Egon.

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