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