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.

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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.

Lymphomas Miner

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According to the Johns Hopkins Lupus Center (https://www.hopkinslupus.org/lupus-info/lifestyle-additional-information/lupus-cancer), lupus patients may experience an elevated risk of lymphoma (Hodgkin and non-Hodgkin) and other types of cancers, such as cancer of the cervix, breast cancer, lung cancer, and endometrical cancer.

We have developed the Lymphomas Miner (http://www.minerazzi.com/lymphomas), a topic-focused search engine, which can be used to find resources relevant to this type of cancer. Its news channel provides access to many news sources on different types of cancers.

You may also recrawl individual search results and build your own curated collection. To do this, just do a search and then click the “links” icon below a given result. You should see a list of internal and external links from that result pointing to new resources, which can then be recursively crawled. A great discovery research tool.

In the pipeline are new miners focused on other types of cancers. A list of topic-specific miners are available from http://www.minerazzi.com/

Extracting Topic-Specific Wikipedia Links

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Below is an illustrative example of a miner for extracting specific links from Wikipedia.

http://www.miislita.com/wikilinks

This miner provides entry points to Wikipedia links relevant to Puerto Rico.

Recrawling a search result discovers new topic-specific links, allowing for further exploration and mining.

Programming Languages Miner

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Programming Languages Miner (http://www.minerazzi.com/programming-languages/)

Find lists of programming languages, tutorials, and related resources.

Recrawl results to build your own curated collection.

Its news channels include direct access to blog feeds of some of the most popular languages, like C++, JavaScript, PERL, PHP, and PYTHON.

Beware of Chemistry Heuristics

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I have added new content to the bond order calculator mentioned at https://irthoughts.wordpress.com/2018/12/20/bond-order-calculator-tool/

The content added is to illustrate the risks of blindly relying on chemistry heuristics and old-school chemistry ideas. Essentially, it is debunked some few old-school chemistry ideas, like

  1. SO3 has a bond order of 2. Really?
  2. nitrogen cannot form five bonds. Really?
  3. octet rule expansion by means of using d orbitals. Really?
  4. bond order is the number of chemical bonds shared by two atoms. Really?

To access this content, visit http://www.minerazzi.com/tools/bond-order/calculator.php

Once there, navigate to the ‘What is computed?’ section, and then to the subsection ‘Beware of Blindly Relying on Chemistry Heuristics’.

Enjoy it.