Quantumbiochemistry.org
The quantum theory applied to biology
Why quantumbiochemistry.org ?
The goal of this site is to demonstrate how quantum mechanics can contribute to the understanding of biochemistry, molecular biology and biology. I am actively doing research on how quantum chemistry can contribute to the progess of bioscience. Content will be added to this site to report new results or conclusions.
I do not yet cover every possible use. Instead I chose to limit myself to chemical bonding and reactivity, more specifically to Lewis acid and base reactions.
The Lewis acid and base concept is particularly useful for our purpose. Lewis acid and base reactions are very common in biology and cover the large majority of the chemistry in biological organisms.
Also they can help us understand enzyme catalysis. Enzymes are real (existing) substances that manipulate atom in an organised way. They are thus potentially a key to the further development of nanotechnology.
Previous research done on this topic
Studies on the reaction mechanism of RNAse T1 with quantum chemical reactivity indexes.
In a nutshell
Molecular Structure Theory
The molecular structure theory is an application of the quantum theory. It defines the Schrödinger equation for a gas of electrons and nuclei. By the way it does not assume that atoms exist.
The solution of this differential equation is a mathematical representation of the molecule called the molecular wave function. In practice we will only calculate the electronic wave function of the molecule. The nuclei are assumed to be in a fixed position.
One must use advanced mathematics to obtain that wave function and we obtain only an approximation of the real electronic wave function. Be aware that the approximation could not be good enough and lead to wrong conclusions.
We provide a summary on molecular structure theory with links to further reading for those who want to get into the details. The tutorial provides insight into the mathematical methods, the assumptions and approximations that have been made.
Lewis acids and bases
This approximate wave function can then be used to calculate derived properties that will give us information about the Lewis acid and base properties of the molecule. These properties can then explain how and why a molecule engages in a chemical reaction.
The how and the why is what we are looking for when doing biochemical research especially when looking at enzyme catalysis. If we understand why and how a chemical reaction occurs then we also understand why and how an atom is manipulated by the enzyme. This in turn might help us with the development of nanotechnology. This reveals a real challenge : how can we manipulate atoms.
Next we provide an article on chemical reactivity and Lewis acid base reactions we explain how chemical reactivity is rooted in molecular structure theory. This is a must read otherwise you will not able to understand the research and its added value.
Chemical software
With our approach to quantum biochemistry anyone with a home computer can do quantum calculations for research, education or personal interest. You don’t need a supercomputer and a whole team of IT experts. That’s why we also have an article about the software that is available free of charge.
There are also libraries availbale for online 3 dimensional viewing. Below we demonstrate this with Rosmaricine.
Rosmaricine is found in rosemary and has anti-inflamatory properties.
Nicholas Rego and David Koes 3Dmol.js: molecular visualization with WebGL Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829Contact Information
Contact Information: please feel free to contact me at info@quantumbiochemistry.org.
I listen to any comments, remarks suggestions. I will try to answer any questions as good as I can.
Copyright© 2023 Demeester Piet