Monday, December 30, 2013

Wolfram|Alpha and chemistry homework problems


Update 2014.01.20: This video really inspired this post and nicely addresses many of the objections one might raise.

About two weeks ago I wrote a blogpost wondering to what extent many chemistry homework problems are rendered trivial by chemical calculators.  As part of the post I started a little experiment where I see how many problems posted on Reddit's Chemhelp page I could solve using such calculators. I subsequently expanded the experiment to include Yahoo Answers chemistry page. Here you can see my contributions for Reddit and Yahoo Answers, but I'll focus on the Yahoo Answers.

As I am writing this I have supplied 21 answers on Yahoo Answers and 11 answers on Reddit (plus 1 in the mathhelp page). All but 3 of the answers involve Wolfram|Alpha (WA) so this is what I'll focus on here.  Most of these questions can be answered in two steps using WA and many can be answered in one step, i.e. one simply reformulates the question, types it in to WA and gets the answer.

Examples of the latter type of question:

"How many grams of sulfur (S) are needed to react completely with 246 g of mercury (Hg) to form mercuric sulfid?" which can be answered by typing the following into WA: "convert 246 g Hg to mercuric sulfid" (which also fixes the spelling).

"Calculate the number of moles of Al2O3 produced from 27.6 moles of O2" => "convert 27.6 moles O2 to Al2O3"

"How many grams of NaOH are in 250 mL of a 3.0 M NaOH solution?" => "convert 250 mL 3.0 M NaOH to grams"

"Na2CO3+Pt(ClO3)2 -> NaClO3 + PtCO3. Balance the equation.?" => "Na2CO3+Pt(ClO3)2 -> NaClO3 + PtCO3"

"C2H6+O2-> CO2+H2O. Draw Lewis dot structures for each species.?" => "lewis structure of CO2"

"Calculate the empirical formula of a molecule with the following percent compositions: 59.7% lithium (Li) and 40.3% nitrogen." => "59.7% lithium and 40.3% nitrogen"

"What is the number of mmoles solute in 2 liters of 0.0555 M KMnO?" => "convert 2 liters of 0.0555 M KMnO to mmoles"

"A 10% kcl solution in water has a density of 1.06/ml'calculate its malarity and malality?" => "convert 10 % KCl to malality"

"the blue color in some fireworks occurs when copper (I) chloride is heated to 1500K and emits a blue light of wavelength 4.50*10^2nm. How much energy does one photon of this light carry?" => "convert 485 nm wavelength to joules"

"What is the amount of substance of hydrogen atoms in 0,50g methane (CH4) and why?" => "how much hydrogen in 0.50 grams of methane"

"If 500 grams of Fe reacts with ample Oxygen according to the following equation: 4Fe + 3O2 = 2Fe2O3 A) How many grams of rust are produced? B) How many grams of Oxygen are needed?" => "how much Fe2O3 from 500 grams Fe"

These questions require a bit more knowledge:

"What mass of phosphorous is required to manufacture 2 metric tons (2000 kg) calcium phosphate?" => "convert 2000 kg calcium phosphate to phosphorous".  By default WA interprets calcium phosphate as hydroxyapatite but alerts you to the fact that tricalcium diphosphate is an alternative.  This is a poorly phrased question.
"E=200 M^ -1 Cm^ -1 A=1 Pathlength=0.5 cm Concentration of protein???" => "beer lambert equation"

"Balance the following redox reactionin basic solution using half reaction method?  O2 + Cr 3+ -> H2O2 + Cr2O7 2- to find how many electrons are lost and gained during the reaction" => "O2 + Cr^3+ + OH- -> H2O2 + Cr2O7^2- + e- + H2O" While not straightforward the equation doesn't balance in WA until OH-, e-, and H2O are put on the correct sides.  So this can really be solved by trial and error, once you know translate "basic solution" into these constituents.

"From 0.65 g CaClx, 1.68 g of silver chloride (AgCl) were obtained. Which one is the formula of the calcium salt?" => "moles of Cl in 1.68 g AgCl" then "moles of Cl in 0.65 g CaCl" and "moles of Cl in 0.65 g CaCl2".  Notice how it becomes trivial to solve this problem by trial an error, compared to setting up an algebraic equation.


I would characterize all but the last three problems as "square root problems": they contain the same educational value as asking "what is the square root of 10?", i.e. close to zero. The only real reason were are assigning these problems is because they were taken from (or "inspired" by) textbook questions that were written before chemical calculators like WA were available.

The thing is tools like WA allows us to assign much more interesting chemistry questions. One of the reasons many students think chemistry is boring is that introductory chemistry often is incredibly boring because we assign boring problems with no real point and (with tools like WA) for no good reason.


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Friday, December 27, 2013

MolCalc and the ideal gas enthalpy and entropy contributions





Here are two videos in which I introduce the enthalpy and entropy contributions for an ideal gas with two concrete examples illustrated using MolCalc. The videos are part of a series that I am working on.


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Wednesday, December 18, 2013

Illustrating enthalpy, entropy, and free energy changes using MD


Here is a video I made that uses an MD simulation I found on Youtube to illustrate enthalpy, entropy, and free energy changes. I also use the simulation in these two videos (here and here) to illustrate enthalpy and entropy changes separately.  The videos are part of a series that I am working on.



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Friday, December 13, 2013

Illustrating energy states and estimating enthalpy changes




Here are two videos in which I use Jmol and Molecular Workbench to illustrate energy states and MolCalc to estimate enthalpy changes. The videos are part of a series that I am working on.


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Tuesday, December 10, 2013

Chemical Calculators and homework problems

Tl;dr: I am looking at questions posted at Reddit's Chemhelp page to see how many can be helped by freely available computational tools. You can see the ongoing experiment here.

Before the general availability of conventional pocket calculators every chemistry student has to be able to compute the values of common mathematical functions such as square roots and logarithmic functions by hand or slide rule. Now we no longer teach this skill which frees up time to focus on chemistry and we can assign harder problems or more problems involving such functions because they can be solved much faster with a calculator.

However, there are now several software packages and phone-apps that can solve chemical problems such as chemical nomenclature or balancing chemical reactions.  However, we are not making use of these tools and spending an inordinate amount of time teaching these concepts. Concepts which are becoming the chemical equivalent of the square root function.  Perhaps we could focus on more interesting chemical problems and leave the memorization and other tedious tasks to the computer. I think chemistry would become a more interesting subject as a result.

To test how far along we are on this path, I am looking at questions posted at Reddit's Chemhelp page to see how many can be helped by freely available computational tools. You can see the ongoing experiment here.

UPDATE 2013.12.25: ... and here on Yahoo Answers.

Please join me!

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Friday, December 6, 2013

Sunday, December 1, 2013

Sunday, November 3, 2013

Sunday, October 13, 2013

Chemistry assignments that use Molecule Calculator (MolCalc)


1. One of the reviewers of our J. Chem. Ed. paper on MolCalc included the following tutorial: Molecular Orbital Calculations of Molecules I.Diatomics, Triatomics and Reactions

2.  n-Butane can exist in two different conformations called gauche and anti (Google butane and conformation).  Use Molecular Calculator to estimate the fraction of molecules in the gauche conformation at 25 $^\circ$C. $\Delta H^\circ$  can be computed as the difference in heat of formation.

3. Estimate $\Delta H^\circ$  the for the following reaction at 25 $^\circ$C

NH$_2$CHO + H$_2$O $\rightleftharpoons$ NH$_3$ + HCOOH

a. Using bond energies
b. Using Molecule Calculator

4. How does the molecular structure determine the rotational entropy?  Find out by constructing a molecule with the largest possible rotational entropy using Molecule Calculator.  The largest value I could find was 133 J/molK.  Can you beat that?

5. How well do the simple solvation models work?
a. Estimate the solvation energy of NH$_4^+$ using MolCalc?
b. What is the polar solvation energy of NH$_4^+$ in water at 25 $^\circ$C assuming that it is spherical?

6. Why do ionic compounds dissolve in water?  Use MolCalc to estimate $\Delta G^\circ$ at 25 oC for the following equilibrium 
 
N(CH$_3$)$_4^+\cdot$Cl$^-$ $\rightleftharpoons$ N(CH$_3$)$_4^+$ + Cl$^-$

a. in the gas phase
b. in aqueous solution

7. Solvent screening: charge-charge interactions are weaker in aqueous solution than in the gas phase.  Compute the difference in G$^\circ$ at 25 $^\circ$C between these two molecules using MolCalc
  
a. in the gas phase
b. in aqueous solution

8. Build a molecule with a solvation energy that is as close to 0 as possible.  The closest I got is -1.3 kJ/  How close can you get? 

If you have other suggestions please leave a comment

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Friday, October 11, 2013

Learn QM/MM from Chris Cramer



Chris Cramer's Essentials of Computational Chemistry is one of the most popular textbooks on the topic. In honor of the 2013 Nobel Prize in Chemistry Chris has made his chapter on QM/MM publicly available for a limited time (Update: this has now expired).

Chris is also active on twitter and I can highly recommend you follow him for a nearly daily dose of witty comment.

Wednesday, October 2, 2013

Computational Chemistry Highlights: September issue

The September issue of Computational Chemistry Highlights is out.

CCH is an overlay journal that identifies the most important papers in computational and theoretical chemistry published in the last 1-2 years. CCH is not affiliated with any publisher: it is a free resource run by scientists for scientists. You can read more about it here.

Table of content for this issue features contributions from CCH editor Steven Bachrach:

Are Bond Critical Points Really Critical for Hydrogen Bonding

Sunday, September 1, 2013

Saturday, August 31, 2013

The Polarity and Solvation option in MolCalc

+Maher Channir, under the capable supervision of MolCalc designer +Jimmy Charnley Kromann, has added a great new feature to the Molecule Calculator, shown in the video below.



Some technical stuff
The solvation energy, molecular surface area, and dipole are computed using the PM3/PCM interface recently implemented in GAMESS by +Casper Steinmann.  The displayed surface, which is slightly different than that used by GAMESS, is computed by JSmol, which also computes the eletrostatic potential based on charges computed by OpenBabel when making a mol2 file.

Friday, August 2, 2013

Computational Chemistry Highlights: July issue

The July issue of Computational Chemistry Highlights is out.

CCH is an overlay journal that identifies the most important papers in computational and theoretical chemistry published in the last 1-2 years. CCH is not affiliated with any publisher: it is a free resource run by scientists for scientists. You can read more about it here.

Table of content for this issue features contributions from CCH editors Steven Bachrach, Ben Corry, Gerald Monard, Dean Tantillo, and Jan Jensen:

Towards First Principles Calculation of Electron Impact Mass Spectra of Molecules

Wednesday, July 24, 2013

A python program for reading coordinates and gradients from a GAMESS output file

Some people liked the previous post on python, so I dusted off this python program for reading locating coordinates and gradients in a GAMESS log file and writing out and .xyz+vib file (to create this post).  I have only used it on this output file, but it should work for other files as well.

Even if you have no interest in .xyz+vib files, the program might be useful as an example of how to locate specific information in a file and read it in. If you have similar programs (or questions) please feel free to share them in the comments

Tuesday, July 23, 2013

Illustrating energy minimization: a simple python program

Here is a simple python program I wrote to illustrate energy minimization.  The program uses steepest descent and a force field to minimize the energy of a water molecule in internal coordinates.

If you have a Mac or Linux machine you already have python installed (Windows users please Google and/or leave a comment).  You can also get an invite for koding.com and run it there. You can run it by opening a terminal and typing "python Emin.py".

Things to play around with (once you have it running): change the starting geometry, step size (c), number of steps (n_steps), try printing out the geometry, energy and gradient for each step.

You can also try to write a similar program for other molecules (like methane), although once you have van der Waals interactions you will probably have to switch to Cartesian coordinates and things get complicated.

Related blog posts
The force is strong in this one
The autoopt tool in Avogadro

Wednesday, July 17, 2013

MOPAC/PCM interface in GAMESS

A new version of GAMESS was released recently.  Among the many new features is +Casper Steinmann's recent work on interfacing the PCM solvation method with the semiempirical methods AM1 and PM3.  So you can now simulate molecules in solution with AM1 and PM3.  

Casper also parallelized AM1 and PM3 (both in gas phase and solution), though molecules have to be pretty big before you see an appreciable speed up, as you can see from the figure below (on small proteins).



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Monday, July 1, 2013

Computational Chemistry Highlights: June issue

The June issue of Computational Chemistry Highlights is out.

CCH is an overlay journal that identifies the most important papers in computational and theoretical chemistry published in the last 1-2 years. CCH is not affiliated with any publisher: it is a free resource run by scientists for scientists. You can read more about it here.

Table of content for this issue features contributions from CCH editors Steven Bachrach, Jonathan Goodman, and Jan Jensen:

Molecularspace.org



Tuesday, June 18, 2013

The 2013 Bjerrum-Brønsted-Lang Lecture: quantum biochemistry and the rise of semiempirical methods and automation in quantum chemistry

2013.06.29 UPDATE: Here's a recording of my talk.  Some more details: I received the A. Tovborg Jensen Award from the Royal Danish Academy of Sciences.  Tovborg Jensen was a Danish chemist who brought crystallography, which he learned from Bragg himself, to Denmark. Upon his death he bequeathed a considerable sum of money to the Royal Danish Academy of Sciences to establish the award and associated lecture series names in honor of his colleagues Niels Bjerrum (he of the Bjerrum length), Johannes Brønsted (Brønsted acid/base theory) and Kaj Linderstrøm-Lang (who coined the terms primary, secondary, tertiary and quaternary protein structure).



This afternoon I am giving the 2013 Bjerrum-Brønsted-Lang Lecture at the University of Copenhagen.  Here are my slides.  I plan to record the talk (using my iPhone) which I will post later.

Saturday, June 15, 2013

Illustrating EFMO fragmentation with Jmol

On Tuesday I am giving a talk and I want to illustrate fragmentation of a protein for the EFMO method.  So I used Jmol to create this movie which I will embed in a Powerpoint slide

The underlying Jmol script is here.  Just paste it in to the Jmol Script Console and record the screen (I used Screenflow, but screencast-o-matic is a free alternative).

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Sunday, June 2, 2013

Molecular Modeling Basics Reviewed on Amazon

cover
Two reviews have appeared on Amazon: one on the Canadian site and one on the American site.  The latter one compares and contrasts MMB to Hincliffe's Molecular Modeling for Beginners.  As always, much appreciated!

Saturday, March 23, 2013

DFT-D, DFT-D2 and DFT-D3: Density functional dispersion correction

Dispersion-corrected DFT, such as B3LYP-D3, are not new functionals but a mix of conventional functionals and an add-on energy term.  For example, B3LYP-D3 denotes a calculation with the usual B3LYP functional plus a D3 dispersion correction energy term.  The dispersion correction energy term is a relatively simply function of interatomic distances and contain adjustable parameters that are fitted to conformational and interaction energies computed using CCSD(T)/CBS.  The fitting is done for a given functional. DFT-D and DFT-D2 energy corrections consider all pairs of atoms while DFT-D3 also consider triplets of atoms to account for three-body effects.

Because the dispersion correction is an add-on term it does not directly alter the wavefunction or any other molecular property.  However, geometry optimizations with dispersion correction will lead to a different geometry than without because the dispersion correction contributes to the forces acting on the atoms.

Dispersion corrections can lead to significant improvements in accuracy and the computational cost associated with dispersion corrections are negligible, so if your favorite code supports dispersion corrections for your functional of choice there is little reason not to use it.

Similar (but not identical) dispersion corrections have also been developed for semi-empirical methods such as PM6, usually in combinations with analogous add-on energy terms to improve hydrogen bonding, e.g. PM6-DH+ and PM6-DH2.

Further reading:
A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu
Dispersion corrections and bio-molecular structure and reactivity

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Thursday, February 28, 2013

The Molecule Calculator v.1.1


+Jimmy Charnley Kromann has put a new version of the Molecule Calculator online.  The main new features are:

1. JSmol instead of Jmol.  This means that MolCalc now works on iPhones and iPads.  The only thing that doesn't seem to work there is measuring distances and angles.  This also means that the load button had disappeared.

2. New starting points for molecule building: the default starting structure is still methane, but this can now now be changed to benzene or the water dimer.  It is also possible to search for other structures using common names or SMILES.

3. One can now compute other thermodynamic properties in addition to the heat of formation.

The guts of the calculations are still the same as for version 1.0 except that the MMFF force field is used for pre-optimization instead of the UFF force field.

As always the source code is available on Github

The development of MolCalc is supported by the University of Copenhagen through the Education at its Best initiative (Den gode uddannelse).

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Sunday, February 3, 2013

Getting started with JSmol

Readers of this blog will know I am quite fond of Jmol. But Jmol uses Java, which has some securities issues and doesn't work on iOS.  Luckily, Jmol has been converted to JavaScript to create a program called JSmol.

JSmol accepts all the same commands as Jmol, but setting up a webpage with JSmol is a little bit different.  Here is a very simple page to help get you started and the HTML code and be found below.

The location of the jsmoltest.html is in my home directory while the jsmol code is in a folder called "jsmol" also sitting in my hope directory.  The jsmol folder is created when you unzip the JSmol zip file you can download here.

The JSmol distribution also includes a simple example of having two JSmol windows on one webpage.  You can find that file here.

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Wednesday, January 23, 2013

Learn computational chemistry from Chris Cramer


Chris Cramer's Essentials of Computational Chemistry is one of the most popular textbooks on the topic.  He has just started teaching Computational Chemistry (CHEM 4021/8021), but this time he is making video presentations of his lectures!

Chris is also active on twitter and I can highly recommend you follow him for a nearly daily dose of witty comment.