April 01, 2024
Science
The Tollens Condensation
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In the Tollens condensation an aldehyde or ketone with at least one α - hydrogen is reacted with formaldehyde and strong base to synthesize diol, triols, or tetrols [ 1 , 2 ]. The reaction...
How long it takes chemical reactions to reach completion
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In this article, I examine the kinetics by which chemical reactions approach completion or equilibrium. I illustrate how the reaction order, reversibility, and rate constants are all important...
February 29, 2024
Benzocaine synthesis from toluene and p-xylene
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Benzocaine is local anesthetic useful as a topical anesthetic and painkiller. In this article I examine two industrially relevant routes to synthesize this drug from widely available petrochemical...
July 16, 2023
The mathematics of compound interest
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A fundamental idea in finance is the time value of money: money now is worth more now than money later. Mathematically, this reality is described by the interest rate. The value of money in the...
December 21, 2022
Dynamic Nuclear Polarization in Solid State NMR
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Nuclear magnetic resonance (NMR) spectroscopy is a powerful tool in elucidating molecular structure and dynamics. It is applied in many areas of science and in medical imaging. In recent decades,...
April 17, 2022
Modelling a multi-state G protein signaling pathway
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G proteins are intracellular signaling molecules whose functions are governed by the GTPase cycle. An important class of G protein activators are guanine nucleotide exchange factors (GEFs), which...
December 18, 2021
Organic synthesis of Aspirin from benzene
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Aspirin (acetylsalicylic acid) is a nonsteroidal anti-inflammantory drug (NSAID) useful for alleviating pain, fever, and inflammation. In addition to being one of the most widely used drugs (44,000...
December 29, 2020
Distinguishing reversible enzyme inhibition mechanisms
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In enzymology, inhibitors are categorized by their kinetic mechanism. In this article, I examine and clarify differences between a few common reversible inhibition mechanisms: competitive,...
September 18, 2020
Total synthesis of metformin
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Metformin is a drug used for treating type 2 diabetes, where it works to lower blood sugar levels. It is chemically unusual because of its remarkably high nitrogen:carbon ratio > 1:1. In this...
August 21, 2020
The difference between Ki, Kd, IC50, and EC50 values
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In biochemistry and pharmacology, a variety of parameters are reported as measures of the potency of enzyme inhibitors/drugs, including Ki, Kd, IC50, and EC50. Though related, their definitions...
December 31, 2019
AZT – mechanism of action and organic synthesis
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Azidothymidine (AZT, also called Zidovudine) is a nucleoside analog reverse-transcriptase inhibitor useful against the HIV virus. It was the first treatment to be developed and is still in use today....
December 21, 2019
Forecasting website ad revenue
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Many websites on the internet are monetized with ads, such as news sites, educational sites, blogs, social media sites, and gaming sites. In this article, I review how website ad revenue is...
June 15, 2019
Km vs Kd - the difference between Michaelis and dissociation constants
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Two commonly encountered parameters in enzyme kinetics are the Michaelis constant (Km) and the dissociation constant (Kd), both report aspects of a substrate’s binding behavior. In this article, I...
February 02, 2019
The relationship between TV screen size and price
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The cost of TVs depends heavily on their size, with larger ones being progressively more expensive. I examine this relationship by aggregating TV price data over a range of sizes and brands. In...
January 03, 2019
Health benefits of green tea – the scientific evidence
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In this article, I review the current scientific evidence concerning green tea’s health effects and their responsible mechanisms of action. Tea is a beverage made from the leaves of the Camellia...
December 22, 2018
Synthesis of ibuprofen from benzene
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Ibuprofen (brand name Advil or Motrin) is one of the most widely used nonsteroidal anti-inflammatory drugs (NSAIDs). It is useful for reducing pain, inflammation, and fever. In this article I examine...
October 11, 2018
The mechanism of action of Eflornithine
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The drug Eflornithine (also called Vaniqa or α-difluoromethylornithine) is a selective inhibitor of the enzyme ornithine decarboxylase (ODC). It is useful in the treatment of African sleeping...
August 25, 2018
The synthesis of sucralose from sucrose
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Sucralose is a widely used artificial sweetener. It is noncaloric, and one of the sweetest sugar substitutes currently available, being around 600 times sweeter than sucrose [ 1 ]. Commercial...
August 19, 2018
Diluting a solution to Avogadro’s limit
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How many atoms/molecules are in a mole? There are precisely 6.022 × 10^23 units (Avogadro’s number). While many are familiar with this number, the true enormity of its size is hard to fully grasp....
August 11, 2018
The affect of mutation rate on evolutionary equilibrium
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Modelling the effect of mutation rate on the equilibrium state of evolving populations.
July 28, 2018
Organic synthesis of indomethacin
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In this article, I explore synthetic routes for the production of indomethacin. Indomethacin (sometimes also called indometacin) is a widely used nonsteroidal anti-inflammatory drug (NSAID). Like...
February 13, 2018
Probing protein-protein interactions in the yeast glycolytic metabolon
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Here I present a proposal for original experimental research, aimed at elucidating the protein-protein interactions of a putative glycolytic metabolon in yeast . Through this I highlight a...
February 01, 2018
Time course enzyme kinetics
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The classical approach to enzyme kinetics is focused on initial reaction rates. In assays enzymes are mixed with substrate at known concentrations and the rate of the catalyzed reaction is...
December 20, 2017
A generalized model for enzymatic substrate inhibition
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Enzymes are biological catalysts, fundamental to the chemistry of life. Broadly, they facilitate conversion of substrates (reactants) into products at greatly accelerated rates. In this article,...
December 15, 2016
The basis of high thermostability in thermophilic proteins
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The range of temperature over which life on Earth thrives is incredible. The majority of organisms are mesophilic, having optimum growth rate at moderate temperature (20 to 45 °C ). In contrast,...
April 21, 2016
First order drug elimination kinetics
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Understanding the kinetics of drug elimination is paramount for the design of appropriate dosage regimens. For most drugs, some minimum concentration is needed to achieve a therapeutic benefit....
January 06, 2016
Improving the efficiency of protein dialysis: constant dialysate replacement
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Dialysis is a purification method commonly used in biochemistry to introduce or remove small molecules from a protein sample. In this technique the protein sample is placed in a dialysis bag...
August 24, 2015
Mathematical modelling of evolution
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The theory of evolution is based on the principle that organisms whose heritable traits confer greater fitness have a greater tendency to survive and reproduce. This notion is often presented and...
July 28, 2015
Calculating the optimum ddNTP:dNTP ratio in Sanger sequencing
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Sanger sequencing is a classical technique to determine the base pair sequence of DNA samples. The technique utilizes modified dideoxynucleotide tripshosphates (ddNTP) which lack a 3’...
February 20, 2015
A mathematical model of hair growth
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In this article, I develop a simplistic mathematical model for the growth of hair. Consider a population of N hairs. Different hairs may have different length (l). Over discrete time intervals (t)...
December 29, 2014
Life does not violate the second law of thermodynamics
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The second law of thermodynamics states that the entropy (S), a measure of disorder, increases during any spontaneous process in an isolated system.
August 23, 2013
Collagen and the importance of vitamin C
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Collagen is the most common protein in humans. There are a dozens of collagen variants found in our connective tissues and cells. It is composed of three repeating amino acids of the form...
August 18, 2013
Temperatures below absolute zero are surprisingly hot
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It is not widely known, but special types of systems are able to have negative absolute temperatures (less than 0 K). At first glance this seems like it violates the third law of thermodynamics which...
August 15, 2013
The molecular difference between heat and work
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Heat and work represent two distinct means by which the internal energy of a system can change. In this article I clarify the fundamental, molecular differences between these two processes....
August 14, 2013