• About IR Thoughts
  • Minerazzi Tools
  • Minerazzi Tutorials

IR Thoughts

~ Thoughts on Information Retrieval, Search Engines. Data Mining, and Science & Engineering

IR Thoughts

Category Archives: chemistry

The Ideal Gas Law Oracle

06 Friday Mar 2020

Posted by egarcia in Algorithms, chemical mining, chemistry, Chemometrics, IR Tools, miner, minerazzi, Programming

≈ Leave a comment

Tags

chemistry, ideal gas law, ideal gas law oracle, oracle

Most online calculators reduce the user experience to returning results in response to some input data. As a tools developer, I know this quite well.

I’ve been asking to myself, “Why not use a different approach and build calculators that behave as oracles?” By an oracle I mean a black box that converts the input data into a user’s question (the query) and the output (the response) into the answer to the question.

To truly behave as an oracle, said tool should also take care of most of the tasks a user is expected to do. The tool should also “react” to mistakes made by a user.

With that in mind, here is my first attempt at turning an online calculator into an oracle-like tool: The Ideal Gas Law Oracle (http://www.minerazzi.com/tools/ideal-gas-law/oracle.php).

This one even takes care of significant figures and unit conversions. Chemistry teachers and students might find it useful. For instance, teachers can use the tool to add content to lecture notes, quizzes, and tests. Students can use it to double-check exercise results from homeworks and textbooks.

The Bond Order Calculator: Updates

14 Thursday Nov 2019

Posted by egarcia in calculators, chemistry, minerazzi

≈ Leave a comment

Tags

Bond Order, bond order calculator, chemistry tools, tools

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.

CUNY Computational Chemistry Tools

03 Thursday Oct 2019

Posted by egarcia in Algorithms, calculators, chemistry, Chemometrics, Data Mining, IR Tools, minerazzi

≈ Leave a comment

Tags

bond order calculator, chemistry tools, computational chemistry, hydrocarbons parser

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.

Beware of Chemistry Heuristics

09 Tuesday Jul 2019

Posted by egarcia in chemistry

≈ Leave a comment

Tags

chemistry, chemistry heuristics

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.

Bond Order Calculator Tool

20 Thursday Dec 2018

Posted by egarcia in Algorithms, calculators, chemical mining, chemistry, Chemometrics, Data Mining, Programming, Software

≈ 3 Comments

Tags

Bond Order, chemistry, Chemistry Calculator, chemistry tools, Diatomic Species

bond-order-example

This bond order tool calculates bond orders of diatomic species with up to 20 electrons, without using Molecular Orbital Theory! It is available at

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

We developed the tool inspired in Dr. Arijit Das set of innovative and time economic formulae for chemical education. His methodologies are suitable for computer-based learning (CBL) activities or for writing computer programs for solving chemistry problems.

Unlike with other bond order calculator tools, to use ours you don’t need to write Lewis structures, and electron configurations, or count electrons, bonds, orbitals, and atoms. Just enter a chemical formula and the tool will do the rest for you.

In my opinion, students who know how to write programs for solving chemistry problems have an edge when taking quantitative courses like analytical chemistry, instrumental analysis, chemometrics, computational chemistry, and similar courses. I think they are better prepared for multidisciplinary research work than those who cannot code.

Developing this tool was really gratifying as the work inspired us to derive an algorithm for predicting number of unpaired electrons and magnetic properties of single atoms, diatomic species, and their ions. Hopefully, this algorithm will be available early next year in the form of a new chemistry calculator.

We are also developing a tool that computes bond orders of all kind of species, including the polyatomic cases.

We are sincerely in debt to Dr. Arijit Das from Ramthakur College, Agartala, West Tripura, India for encouraging us to develop this tool for educators, scholars, and chemistry students.

Note:

This tool, as our Hydrocarbons Parser (http://www.minerazzi.com/tools/hydrocarbons/parser.php) is listed in the City College Chemistry Web Resources Guide at CUNY. Find them both in the guide Computational Chemistry category (https://library.ccny.cuny.edu/chemistry/computational)

Hybrid Similarity Search (HSS) Algorithm for Chemistry Searching

14 Sunday Oct 2018

Posted by egarcia in chemical mining, chemistry, Chemometrics, Data Mining, information retrieval, IR Tools, miner, minerazzi, New Information Retrieval Paradigms, Queries, Vector Space Models

≈ Leave a comment

Tags

Cheminformatics, chemistry, chemistry tools, Chemometrics

Hybrid Similarity Search (HSS) Algorithm for Chemistry Searching for Fentanyl-related compounds and other drugs.
Free version: https://www.mswil.com/images/NIST/NIST17/GCMS-Hybrid-Search-AnalChem-2017.pdf

This is a news from NIST back in March (https://www.nist.gov/news-events/news/2018/03/free-software-can-help-spot-new-forms-fentanyl-and-other-illegal-drugs ) and found with the NIST RSS channel of the Chemical Substances Miner http://www.minerazzi.com/chemsubstances/spp.php

It is a nice example of Information Retrieval applied to Chemistry. They used a modified cosine similarity function. I see possible applications to topic analysis.

Original Source:
https://pubs.acs.org/doi/abs/10.1021/acs.analchem.7b03320
Anal. Chem., 2017, 89 (24), pp 13261–13268 DOI: 10.1021/acs.analchem.7b03320

Abstract:
“A mass spectral library search algorithm that identifies compounds that differ from library compounds by a single “inert” structural component is described. This algorithm, the Hybrid Similarity Search, generates a similarity score based on matching both fragment ions and neutral losses. It employs the parameter DeltaMass, defined as the mass difference between query and library compounds, to shift neutral loss peaks in the library spectrum to match corresponding neutral loss peaks in the query spectrum. When the spectra being compared differ by a single structural feature, these matching neutral loss peaks should contain that structural feature. This method extends the scope of the library to include spectra of “nearest-neighbor” compounds that differ from library compounds by a single chemical moiety. Additionally, determination of the structural origin of the shifted peaks can aid in the determination of the chemical structure and fragmentation mechanism of the query compound. A variety of examples are presented, including the identification of designer drugs and chemical derivatives not present in the library.”

Chemistry Organizations Miner

02 Sunday Sep 2018

Posted by egarcia in chemical mining, chemistry, Crawlers, Curated Collections, Data Mining, IR Tools, miner, minerazzi, News

≈ Leave a comment

Tags

Chemistry Collections, Chemistry Organizations, Chemistry Student Organizations, miner, minerazzi

Chemistry Organizations Miner

The Chemistry Organizations Miner (http://www.minerazzi.com/chemorgs/) is our newest productivity-driven search engine.

This micro-index helps you find worldwide chemistry organizations, societies, industry groups, chemistry student organizations, and more.

Its news channels can help you search for research, articles, events, and other types of news relevant to chemistry.

Recrawl its search results and build your own curated collection of resources about chemistry organizations.

Chemometrics Miner

07 Saturday Jul 2018

Posted by egarcia in chemical mining, chemistry, Chemometrics, Curated Collections, Data Mining, information retrieval, IR Tools, miner, minerazzi

≈ Leave a comment

Tags

Chemical data mining, Cheminformatics, Chemometrics, Chemometry, minerazzi, miners

Chemometrics, our newest miner.
http://www.minerazzi.com/chemometrics

 

Find tools, techniques, and tutorials for extracting information from chemical systems.

Recrawl search results and build your own curated collection on chemometrics, cheminformatics, and chemical data mining.

Access news relevant to chemometry.

 

A Tutorial on Polynomial Regression through Linear Algebra

22 Sunday Apr 2018

Posted by egarcia in Algorithms, bioinformatics, chemical mining, chemistry, Correlation Coefficients, Data Mining, Mathematics, Statistics and Mathematics

≈ Leave a comment

Tags

Algorithms, Linear Algebra, Mathematics, Matrices, Polynomial Regression, Regression, tools, tutorials

If you are a chemist, biodesigner, or a researcher working in other fields, eventually you may need to fit a paired data set to a polynomial regression model. You could use software to do that, or build your own solution. This tutorial is aimed at those interested in the latter. Access it now at

Click to access polynomial-regression-tutorial.pdf

Three different methods for implementing polynomial regression are described. Teachers and students might benefit from the tutorial since the calculations can be done with a spreadsheet software like Excel, by writing a computer program, or with a programmable calculator.

 

 

Acid-Base Systems Tool

10 Wednesday May 2017

Posted by egarcia in Algorithms, calculators, chemical mining, chemistry, Data Mining, Mathematics, Software

≈ Leave a comment

Tags

chemical mining, chemistry, chemistry mining, chemistry tools

This is a new tool, available now at

http://www.minerazzi.com/tools/acid-base-systems/calculator.php

The tool replaces a previous one (removed from the web) where only simple acid-base solutions were considered.

The current one is not limited to the analysis of one solution or to acid-base titrations. Actually the tool also supports pH calculations of systems not undergoing titrations.

This is a great tool for real world applications like pH calculations from natural acid-base systems where a sample might consist of multiple acids mixed with several bases and/or their salts.

Examples of such systems are bio-samples (blood, saliva…) as well as geo-samples (sea and river water) and urban samples (sewage, wastewater,..).

This new tool is based on a general equation for acid-base systems that is solved using a residual analysis algorithm, avoiding the need for using inversion techniques, successive approximations, Newton-Raphson method, or the evaluation of derivatives or high-degree polynomials.

← Older posts
January 2021
M T W T F S S
 123
45678910
11121314151617
18192021222324
25262728293031
« Sep    

Favorite Sites

  • Minerazzi.com

Pages

  • About IR Thoughts
  • Minerazzi Tools
  • Minerazzi Tutorials

Categories

  • 4D Printing
  • AIRWeb Course
  • Algorithms
  • Amazon Alexa
  • Android
  • Arithmetic Geometry
  • Best Match Models (BM)
  • Big Data
  • BioDesign
  • bioinformatics
  • Blogroll
  • calculators
  • Cancer
  • Cancer Research
  • Causality & Determinism
  • Chaos
  • chemical mining
  • Chemist Biographies
  • chemistry
  • Chemometrics
  • Clinical Trials
  • Cloud Computing
  • Conferences
  • coronavirus (COVID-19)
  • Correlation Coefficients
  • Cortana
  • cosine similarity
  • Crawlers
  • Curated Collections
  • Data Conversion
  • Data Mining
  • Data Structures
  • Deep Neural Networks
  • directories
  • Directories
  • Docker
  • Dynamics
  • Favorite Sites
  • Feed Tools
  • Fisher Transformations
  • Fractal Geometry
  • Fractal Patterns
  • google
  • Graduate Courses
  • Hacking
  • Homeland Security
  • Human-Computer Interaction
  • Image Compression
  • information retrieval
  • Internet Engineering
  • Internet of Senses
  • Internet Standards
  • inverted index
  • ir
  • IR Quizzes
  • IR Tools
  • IR Tutorials
  • Kubernetes
  • Latent Semantic Indexing
  • Legacy Posts
  • LIGO
  • Machine Learning
  • Marketing Research
  • Mathematics
  • Medical Cannabis
  • meta-analysis
  • Mind Retrieval
  • miner
  • minerazzi
  • Miscellaneous
  • National Laboratories
  • New Information Retrieval Paradigms
  • News
  • Newsletters
  • Nonlinear Dynamics
  • One-to-Many (O2M)
  • Open Source Projects
  • PageRank
  • Patents
  • PCA
  • People Searches
  • Perfectoid Spaces
  • PHP
  • Physiology
  • Poems
  • political networks
  • Predatory Conferences
  • Predatory Journals
  • Programming
  • Public Databases
  • Public Records
  • Quack Science
  • Quantum Computing
  • Quantum Information Retrieval
  • Quantum Searches
  • Quantum Theory
  • Queries
  • Ranking Results
  • Research Centers
  • RSS/Atom Feeds
  • Scripts
  • search engines
  • Search Engines Architecture Course
  • Search Modes
  • self-weighting
  • SEO Myths
  • Sitemaps
  • social mining
  • social pulse parser
  • Software
  • Spam
  • Statistics and Mathematics
  • SVD
  • Technology Inventions
  • Theoretical Physics
  • Theses
  • twitter
  • URLs Mining
  • Vector Space Models
  • Voice Assistants
  • Web Mining
  • Web Mining Course
  • Web Security
  • Xamarin

Recent Posts

  • On Fake Research, “Academic” Spam, and ASEO
  • The Almost Binary Heuristic
  • Vector Space Explorer Tool
  • Revamping the Cosine Similarity Calculator Tool
  • RAR Parser |An RSS, ATOM, and RDF Parser
  • Latent Simplex Position Model
  • Coronavirus (COVID-19) Miner
  • The Ideal Gas Law Oracle
  • Weighted Averages of Correlation Coefficients
  • On the Internet of Senses and Cyborg Organoids
  • Internet of Senses Miner
  • On the Myth of d Orbitals Hybridization
  • The Bond Order Calculator: Updates
  • Semantic Similarity of Healthcare Data
  • Going the multidisciplinary way

Archives

  • September 2020
  • July 2020
  • June 2020
  • April 2020
  • March 2020
  • February 2020
  • January 2020
  • November 2019
  • October 2019
  • September 2019
  • August 2019
  • July 2019
  • June 2019
  • May 2019
  • April 2019
  • March 2019
  • February 2019
  • January 2019
  • December 2018
  • November 2018
  • October 2018
  • September 2018
  • August 2018
  • July 2018
  • June 2018
  • May 2018
  • April 2018
  • March 2018
  • February 2018
  • January 2018
  • September 2017
  • August 2017
  • July 2017
  • June 2017
  • May 2017
  • April 2017
  • March 2017
  • February 2017
  • January 2017
  • December 2016
  • November 2016
  • October 2016
  • September 2016
  • August 2016
  • July 2016
  • June 2016
  • May 2016
  • April 2016
  • March 2016
  • February 2016
  • January 2016
  • December 2015
  • November 2015
  • October 2015
  • September 2015
  • August 2015
  • July 2015
  • June 2015
  • May 2015
  • April 2015
  • March 2015
  • February 2015
  • January 2015
  • December 2014
  • November 2014
  • October 2014
  • September 2014
  • August 2014
  • July 2014
  • June 2014
  • May 2014
  • April 2014
  • March 2014
  • January 2014
  • December 2013
  • November 2013
  • October 2013
  • September 2013
  • August 2013
  • July 2013
  • May 2013
  • April 2013
  • March 2013
  • February 2013
  • January 2013
  • December 2012
  • November 2012
  • October 2012
  • September 2012
  • August 2012
  • July 2012
  • June 2012
  • May 2012
  • April 2012
  • March 2012
  • February 2012
  • January 2012
  • December 2011
  • November 2011
  • October 2011
  • September 2011
  • August 2011
  • July 2011
  • June 2011
  • May 2011
  • April 2011
  • February 2011
  • January 2011
  • December 2010
  • November 2010
  • October 2010
  • September 2010
  • August 2010
  • July 2010
  • June 2010
  • May 2010
  • April 2010
  • March 2010
  • February 2010
  • January 2010
  • December 2009
  • November 2009
  • October 2009
  • September 2009
  • August 2009
  • July 2009
  • June 2009
  • May 2009
  • April 2009
  • March 2009
  • February 2009
  • January 2009
  • December 2008
  • November 2008
  • October 2008
  • September 2008
  • August 2008
  • July 2008
  • June 2008
  • May 2008
  • April 2008
  • March 2008
  • February 2008
  • January 2008
  • December 2007
  • November 2007
  • October 2007
  • September 2007
  • August 2007
  • July 2007
  • June 2007
  • May 2007
  • April 2007

Algorithms calculators chemical mining Conferences Data Mining Hacking Homeland Security Human-Computer Interaction IR Tools IR Tutorials Latent Semantic Indexing Machine Learning Marketing Research Mathematics miner minerazzi Miscellaneous New Information Retrieval Paradigms News Newsletters Programming Queries Scripts Search Engines Architecture Course SEO Myths Software Spam Statistics and Mathematics Vector Space Models Web Mining Course

Create a free website or blog at WordPress.com.

Cancel
Privacy & Cookies: This site uses cookies. By continuing to use this website, you agree to their use.
To find out more, including how to control cookies, see here: Cookie Policy