On the Myth of d Orbitals Hybridization

With regard to the myth, taught to entire generations of chemistry students and perpetuated online in chemistry portals and by outdated tutorials, textbooks, and in classroom lectures, that elements beyond the second period can expand their octet by utilizing available d orbitals, consider this:

Since the 90’s, quantum chemists have shown this idea to be experimentally incorrect as it is energetically unfeasible to use d-orbitals for extra bonds (Kalemos & Mavridis, 2011; Durrant, 2015; Cowley, 2015; Northumbria, 2015). Indeed, the possibility of extensive d-orbital participation has been discredited more than a quarter century ago (Reed & Schleyer, 1990; Magnusson, 1990). As back then Cooper, Cunnigham, Gerratt, Karadakov, & Raimondi stated in a JACS article published by the ACS (Cooper et. al, 1994):

“Indeed, models based on d2sp3, dsp2, and dsp3 hybrid orbitals are still in widespread use among professional chemists and are described in many of the most widely used textbooks. It is tempting to speculate as to why such models continue to survive when there is so much theoretical evidence which does not support them.”

See references below. Additional references, links, and topic discussion are given at http://www.minerazzi.com/tools/bond-order/calculator.php

References

Cooper, D. L., Cunnigham, T. P., Gerratt, J., Karadakov, P. B., & Raimondi, M. (1994). Chemical Bonding to Hypercoordinate Second-Row Atoms: d Orbital Participation versus Democracy. J. Am. Chem. Soc. Vol. 116, No. 10, pp 4414-4426. doi: 10.1021/ja00089a033.

Kalemos A. & Mavridis, A. (2011). Myths and Reality of Hypervalent Molecules. The Electronic Structure of FClOx, x = 1-3, Cl3PO, Cl3PCH2, Cl3CClO, and C(ClO)4. J. Phys. Chem., 115, (11), pp 2378-2384.

Magnusson, E. (1990). Hypercoordinate molecules of second-row elements: d functions or d orbitals?. J. Am. Chem. Soc., Vol. 112, No. 22, pp. 7940-7951.

Reed, A. E. & Schleyer, P. V. R. (1990). Chemical bonding in hypervalent molecules. The dominance of ionic bonding and negative hyperconjugation over d-orbital participation. J. Am. Chem. Soc., 112, pp. 1434-1445.

The Bond Order Calculator: Updates

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New content was added to the bond order calculator page discussed at

https://irthoughts.wordpress.com/2018/12/20/bond-order-calculator-tool/

and available at

http://www.minerazzi.com/tools/bond-order/calculator.php

Enjoy it.

Semantic Similarity of Healthcare Data

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In “Aggregating the syntactic and semantic similarity of healthcare data towards their transformation to HL7 FHIR through ontology matching“, published in the International Journal of Medical Informatics 132:104002 DOI: 10.1016/j.ijmedinf.2019.104002, Kiourtis et al. (2019), address the following objective, and quote:

“Healthcare systems deal with multiple challenges in releasing information from data silos, finding it almost impossible to be implemented, maintained and upgraded, with difficulties ranging in the technical, security and human interaction fields.”

The authors propose an elegant mechanism “that promises healthcare interoperability through the transformation of healthcare data into the corresponding HL7 FHIR structure.”

These are great news! Very cool and practical research that can solve so many problems in the healthcare informatics field.

Many thanks for citing our cosine similarity tutorial as reference 52.

My only reserve with the paper is that early in the article they suggest adding and averaging similarities, which is a mathematically invalid exercise. Distances are arithmetically additive, but similarities (of the same or different kind or source) are not. We can make similarities additive and average them, but not in the arithmetic sense. Other than that, they work is a noble effort.

Going the multidisciplinary way

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In the paper, “Development of gene-based molecular markers tagging low alkaloid pauper locus in white lupin (Lupinus albus L.)”, published online on 08-13-2019 in Journal of Applied Genetics, Springer (https://link.springer.com/content/pdf/10.1007%2Fs13353-019-00508-9.pdf), the authors computed the Sokal-Michener (simple matching) and Rogers-Tanimoto coefficients with our Binary Similarity Calculator (http://www.minerazzi.com/tools/similarity/binary-similarity-calculator.php), which computes 72 different resemblance (similarity) measures.

I’m so happy to know that more and more researchers across disciplines are finding new uses for this free-to-use tool.

Building these types of tools are always fun, but are even more gratifying when these provide that extra handy help to other researchers. That’s why I decided to go the multidisciplinary way in the sciences. Their success is my success.

CUNY Computational Chemistry Tools

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If you are a chemist, PhD, or student looking for tools in said discipline, you may want to check the City College Chemistry Web Resource Guide, part of the City College of New York Libraries at CUNY. This is an excellent repository of chemistry resources.

This fall, the college redesigned the site so the web address of the computational chemistry section is now https://library.ccny.cuny.edu/chemistry/computational

Happy to know that two of our chemistry tools are still listed there:

The Bond Order Calculator — http://www.minerazzi.com/tools/bond-order/calculator.php Computes bond orders of diatomic species and their ions having up to 20 electrons, including number of bonding and anti-bonding electrons, without using Molecular Orbital Theory (MOT).

The Hydrocarbons Parser http://www.minerazzi.com/tools/hydrocarbons/parser.php — Calculates boiling points and indicates sigma, pi, single, double, and triple bonds for hydrocarbons, again without using MOT.

I wish that more universities follow in the steps of CUNY and be willing to put together similar repositories, I mean computational chemistry tools, for the benefit of their students and faculties.

Why I chose to be a multidisciplinary scientist?

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When you are a multidisciplinary scientist or teacher, one way of measuring your success is by looking at what students and others in different fields and countries do with the tools and resources you develop. Satisfaction goes all the way up when these help make a difference in their life.

I’m happy to know that in his 2018 PhD thesis “On Enhancing the Security of Time Constrained Mobile ContactlessTransactions” (https://pure.royalholloway.ac.uk/portal/files/33898207/Iakovos_Gurulian_PhD_Thesis.pdf), the author, Iakovos Gurulian from the Information Security Group, Department of Mathematics at the prestigious Royal Holloway, University of London, developed a Python program capable of running our Binary Similarity Calculator (http://www.minerazzi.com/tools/similarity/binary-similarity-calculator.php), which computes 72 different similarity measures. See pages 87-89, tables 4.1 and 4.2, and reference 118 of the thesis.

The Tutorial on Distance and Similarity (http://www.minerazzi.com/tutorials/distance-similarity-tutorial.pdf) was also cited as reference 60.

According to https://www.topuniversities.com/, Royal Holloway ranks 6/10 in London and 291/1000 in the world. Famous for its Founder’s Building, one of the most spectacular university buildings in the world, the College was officially opened by Queen Victoria in 1886.
https://www.topuniversities.com/sites/default/files/royal-holloway-university-of-london.jpg

A Simple Example of Phonetic Similarity vs. Text Similarity

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The followings sound the same so their phonetic similarity is 1.

(a) r u?
(b) ar u?
(c) are u?
(d) r you?
(e) ar you?
(f) are you?

However, the Levenshtein Distance (LD) and Levenshtein Similarity (LS) of (a) with the other strings differ:

LD(a, b) = 1; LS(a, b) = 0.5
LD(a, c) = 2; LS(a, c) = 0.33
LD(a, d) = 2; LS(a, d) = 0.33
LD(a, e) = 3; LS((a, e) = 0.25
LD(a, f) = 4; LS(a, f) = 0.2

Can you find LD and LS results for other possible combinations?

For i = j, LD(i, j) = 0 and LS(i, j) = 1 so you may want to ignore this case.

Note: LD and LS results were computed with our tool at http://www.minerazzi.com/tools/levenshtein/levenshtein-distance-calculator.php

References
http://www.minerazzi.com/tutorials/levenshtein-distance-tutorial.pdf
http://www.minerazzi.com/tutorials/distance-similarity-tutorial.pdf

Zillman’s 2019 Directory of Directories

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Zillman’s 2019 Directory of Directories is a handy resource for those interested in finding specialized gateways to the Web.

Glad to know that this summer Minerazzi was included in the Academic/Education section.

(http://columns.virtualprivatelibrary.net/2019_Directory_Of_Directories_June19_column.pdf)

See also http://www.2019directoryofdirectories.com/

Since 2018 we are listed in the Bot and Intelligent Agent Resources category and few other sections, but did not realize that in that one too.

(http://www.zillman.us/minerazzi-your-search-and-mine)

Cool!

More on Perfectoid Spaces

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Back in 08-12-2018, we blogged on Peter Scholze’s 2011 thesis on Perfectoid Spaces, one of the hottest topics that is taking Mathematics by storm (https://irthoughts.wordpress.com/2018/08/12/peter-scholze-and-perfectoid-spaces-a-math-genius-among-us/).

An introductory discussion on the topic is available at https://mathoverflow.net/questions/65729/what-are-perfectoid-spaces?rq=1

Possible connections and applications are mentioned at https://irthoughts.wordpress.com/2018/08/23/perfectoid-spaces-arithmetic-geometry-and-quantum-theory/.

The Perfectoid Spaces miner is available since 08-16-2018 (https://irthoughts.wordpress.com/2018/08/16/perfectoid-spaces-miner/).

Resources in spanish were added to the miner yesterday 08-26-2019, about a year later. Better late than never.