## 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.

## Sunday, December 8, 2013

### 2013 Nobel Prize Lectures in Chemistry

You can also get Warshel's lecture slides here

## Friday, December 6, 2013

### Illustrating dynamic equilibrium

Here is a video in which I use Molecular Workbench to illustrate dynamic equilibrium.  The video is part of a series that I am working on.

## Sunday, December 1, 2013

### Computational Chemistry Highlights: November issue

The November 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 and Jan Jensen:

Comparison of Molecular Mechanics, Semi-Empirical, Quantum Mechanical, and Density Functional Theory Methods for Scoring Protein−Ligand Interactions

## Sunday, November 3, 2013

### Computational Chemistry Highlights: October issue

The October 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, Grant Hill and Jan Jensen:

## 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?