CUNY Computational Chemistry Tools

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.

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Beware of Chemistry Heuristics

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

Tags

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

This tool computes bond orders of diatomic species having 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 calculators, 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 might be 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

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

Tags

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

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

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

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

http://www.minerazzi.com/tutorials/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

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.

Activity Coefficient Models Calculator

Tags

activity coefficient models, activity coefficients, chemical mining, chemistry, chemistry calculators, chemistry tools, computational chemists, electrochemistry

This is a new tool available at

http://www.minerazzi.com/tools/activity-coefficients/calculator.php

If you are into chemical data mining, this post might interest you.

This new Minerazzi tool easily solves activity coefficient models for a missing term.

Thus the tool allows you to cross-map activity coefficients to ionic strengths and vice versa using the following models:

Debye-Hückel Limiting Law

Debye-Hückel Extended Limiting Law

Güntelberg

Davis

Truesdell-Jones

The tool , written in PHP, was inspired in the WATEQF program originally written in FORTRAN (https://www.nrc.gov/docs/ML0331/ML033170395.pdf).

Recent versions of that program are available for download from the U.S. Geological Survey site at https://wwwbrr.cr.usgs.gov/projects/GWC_chemtherm/software.htm

Chemistry researchers, teachers and students can benefit from this tool, which is part of an ongoing effort of making available online scientific research tools across different disciplines.

04-05-2017 Update: Additional content and literature references added.

Physiology and Chemistry Tools

Tags

chemistry, chemistry tools, Physiology, physiology tools, tools

Recent available tools relevant to physiology and chemistry, with some interesting exercises.

Body Mass Index (BMI)
http://www.minerazzi.com/tools/body-mass-index/calculator.php

Corpulence Index (CI)
http://www.minerazzi.com/tools/corpulence-index/calculator.php

Membrane Potentials
http://www.minerazzi.com/tools/membrane-potentials/calculator.php

Cell Electrode Potentials
http://www.minerazzi.com/tools/cell-electrode-potentials/calculator.php

Standard Electrode Potentials
http://www.minerazzi.com/tools/standard-electrode-potentials/calculator.php