At Play With GAMESS (4)

Another in my GAMESS series on quantum chemistry. GAMESS is unquestionably a magnificent piece of work. All the people who have produced it should be very proud. With the steady improvement of my skill using GAMESS, I was able to find the chemical reaction I was looking for in that earlier post. The basis set […]

At Play With GAMESS (3)

The results of some calculations just need to be showcased. This ab initio chemical reaction simulation took a huge amount of time and effort to generate. Depicted here is an attack by hydroxide (-1 charge) on aminophosphate (-2 charge). The black ball is phosphorous, red is oxygen, white is hydrogen and blue is nitrogen. As […]

At Play With GAMESS (2)

Rather than make a post that is six miles long with updates, new posts with new content seem like a good idea. For most people this would be an easy idea! I’ve continued to learn with GAMESS. The functionality that interests me the most is the capacity to use the background of automated quantum mechanical […]

The Organic Chemistry Lie

Fallout from my learning about Molecular Orbital theory and Hartree-Fock. I’ve said repeatedly that Organic Chemistry is along the spectrum of pursuits that uses Quantum Mechanics. Organic Chemists learn a brutal regimen of details for constructing ball-and-stick models of complicated molecules. I’ve also recently discovered that chemistry –to this day– is teaching a fundamental lie […]

Building a Molecule; Time Spent in the Gap

How is a molecule built? Rather, what exactly is required to predict the electronic structure of a molecule using modern tools? I will use this post to talk about my time spent learning how to apply the classic quantum mechanical calculation of Hartree-Fock (note, this is plain old Hartree-Fock rather than multi-configuration Hartree-Fock or something […]

The Quantum Mechanics in the Gap

A big cat’s paw of mine is trying to fill the space between my backgrounds to understand how one thing leads to another. When a biochemist learns quantum mechanics (QM), it happens from a background where little mathematical sophistication is required; maybe particle-in-a-box appears in the middle of a low grade Physical Chemistry class and […]