As the clusters begin to increase in size, only a small amount of the molecules will get burned, as the rest will go out the exhaust as unburned fuel and smoke.
Its estimated that eight out of every ten diesel engine failures are directly related to poor quality and contaminated fuel. The build up of contamination in the fuel systems and storage tanks can clog filters, thereby causing the engine to shut down, and damage to the engine to occur.
The number one reason for bad fuel is due to the increasing popularity of diesel power and the accompanying increased demand for more diesel fuel. Long ago, diesel fuel remained in the refinery storage tanks long enough to naturally seperate and begin to settle, allowing the clean fuel to be drawn apart.
Now, with the demand getting higher than ever, the fuel is never stationary long enough to settle, and the suspended water and solids are passed on to the person buying the fuel - you.
The changes in refinery techniques is also a problem. In order to get more products, diesel fuel is being refined for more marginal portions of the crude barrel. This results in a lower grade product that is thicker and also contains a lot more contamination.
As time passes and technology gets better and better, one can only hope that the quality of diesel fuel improves. As it stands now, the quality isn't good at all. If you run diesel fuel, all you can basically hope for is that the fuel you are getting isn't contaminated.