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This study investigated production of biodiesel from non edible oil seeds of Jatropha curcas and neem. This is with a view to compare which of the oils when used for biodiesel production is more environmentally friendly and cheap-er. The optimum reaction time for transesterification of Jatropha curcas oil to biodiesel was recorded to be 3h while that of neem oil to biodiesel was 2h. This reduces the operating cost of neem biodiesel. Fatty acid methyl esters (FAME) yield of 86.61% with a viscosity of 5.64 cSt was obtained for Jatropha biodiesel using the established operating conditions. This viscosity was used as an index for maximum conversion of biodiesel (BD) for neem oil. The viscosity obtained for neem oil biodiesel was 5.51cSt. An attempt to increase the reaction time does not give any significant difference in the viscosity. Experimental investigations of the different blends of biodiesel from the two oils were tested on an internal combustion engine. The emissions of different blends showed that neem biodiesel has lower emissions of CO and NOX than Jatropha biodiesel, but CO emissions of Jatropha biodiesel are lower than that of diesel fuel. The NOX value of petrol diesel is higher than B10 – B50 and B10 – B80 of Jatropha and Neem biodiesel respectively. However, NOX values of B60 – B100 and B90 – B100 of Jatropha and neem biodiesel are in the range of 5.27 – 10.74% and 1.39 – 11.93% higher than petrol diesel respectively. The physical properties of both biodiesel met the ASTM standard of D-6751.