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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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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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

This blogpost contains some useful hints for part b. 

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

This blogpost contains some useful hints for part b. 

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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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.

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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Peer instruction questions for very basic molecular quantum mechanics

As I mentioned in my previous blog post I this year I made some screencasts of lectures to free up time for peer instruction questions.  Here are the peer instruction questions I used.

Peer instructions questions for basic quantum mechanics from molmodbasics

This time I tried Socrative for voting, which allows students to type in short answers to questions.  I can then select some of the questions and have students vote on their favorite.  This is what's happening in slide 13 and 23.

You'll notice I also made use of Molecule Calculator, which is introduced here.  Next year I have to remember also to assign the MolCalc intro video.




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The Molecule Calculator

What is MolCalc?
MolCalc is a web interface that allows anyone to build (small*) molecules and estimate** molecular properties such as molecular structure, heats of formation, vibrational frequencies and vibrational modes, and molecular orbitals and orbital energies in a matter of seconds or minutes - depending on the size.  

MolCalc is designed for teaching as opposed to research - specifically for assignments in which students build their own molecules and estimate their own molecular properties.  (**MolCalc is therefore designed to run fast and the estimated molecular properties will not match experimental values exactly, and in some cases be quite different.)  The idea is to have students develop a “chemical intuition” about how molecular structure affects molecular properties, without performing the underlying calculations by hand (which would be near impossible for all but the simplest chemical systems).

How can I use MolCalc in teaching?
Just like a pocket calculator or a symbolic math program (such as Mathematica or MAPLE), MolCalc allows one to assign “higher level” chemical problems that are not practically possible to solve otherwise.  

For example, one might now ask students to compute the effect of a substituent on a particular vibration, and then rationalize the effect using molecular orbitals.  Or one might ask more open ended questions such as “build a molecule with an unusually long C-C single bond”.

How does MolCalc work?
In the Molecule Editor page the molecular structure is build using Jmol and energy minimized using the UFF force field as implemented in Jmol.

In the Molecule Calculator page the structure is re-optimized at the PM3 level of theory for a maximum of 50 steps.  This structure is then used to compute the heat of formation or vibrational frequencies at the PM3 level of theory, or the molecular orbitals using the RHF/STO-3G level of theory.  These calculations are performed with the GAMESS program. OpenBabel is used to manage input files and coordinate files.

*MolCalc 1.0 allows calculations on (closed shell) molecules with only doubly occupied molecular orbitals and with less than 11 non-hydrogen atoms.

Can I modify and/or install MolCalc on my own server?
Yes, MolCalc is distributed through github under the GPL license (

https://github.com/jensengroup/molcalc

). You must obtain a copy of the GAMESS code separately from http://www.msg.ameslab.gov/gamess/download.html

The interface code uses PHP5, jQuery, HTML5, and CSS3 and is very modular.  It therefore quite easy to add new capabilities to MolCalc.

What if I find a bug in MolCalc?
Please report it here.
Who is involved with MolCalc?
MolCalc 1.0 is written by Jimmy Charnley Kromann based on an idea by Jan Jensen. Toke Fritzemeier wrote an early prototype.  The Molecule Editor was inspired, in part, by the Virtual Molecular Modeling Kit.

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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