Selective biodegradation of extended hopanes to 25-norhopanes in petroleum reservoirs. Insights from molecular mechanics

In-reservoir microbial removal of the C-25 methyl group from the extended 17α,21β(H)-hopanes (hopanes) generates 25-norhopanes in crude oils from the West Siberia and San Joaquin basins. This C-25 demethylation occurs preferentially among low molecular-weight hopanes (e.g. C31), while higher homologs are progressively more resistant. Conversion of each hopane to its corresponding 25-norhopane occurred without significant side products and was incomplete at the time of sampling. This is indicated by the match between reconstructed C31---C35, hopane distributions for heavily biodegraded oils (sum of hopane parent and 25-norhopane product for each homolog) and those of related, nonbiodegraded oils. C-25 demethylation favors 22S epimers of the C31, and C32, hopanes compared to 22R, while the opposite applies to the C34, and C35, hopanes, because molecular shapes, dimensions, and volumes vary with stereochemistry at C-22. For example, geometry-optimized C31, and C32, 22S hopanes from molecular mechanics force field calculations are more voluminous, while the C34, and C35, 22S hopanes are less voluminous than their 22R counterparts. The C31, to C35, hopane 22S and 22R epimers show distinct “scorpion-” vs. “rail-shaped” conformations respectively, controlled by different 21-22-29-31 and 17-21-22-30 torsion angles. Because 22S epimers of the extended hopanes tend to favor the scorpion conformation, which folds the side chain back toward position C-25, longer side chains may increasingly hinder C-25 from enzymatic attack. Biodegradation can adversely affect the use of %22S/(22S + 22R) ratios for hopanes to assess thermal maturity. The 25-norhopane ratio improves our ability to distinguish different levels of biodegradation among heavily degraded oils where C-25 demethylation has occurred.