The invention provides novel catalysts and methods of using catalysts for controlling the position of a double bond and cis/trans-selectivity in isomerization of terminal alkenes to their 2-isomers. Catalysts such as (pentamethylcyclopentadienyl)Ru formulas 1 and 3 having a bifunctional phosphine can be used in the methods. A catalyst loading of 1 mol % of formulas 1+3 can be employed for the production of (E)-2-alkenes at 40-70° C.; lower temperatures can be used with higher catalyst loading. Acetonitrile-free catalysts can be used at lower loadings, room temperature, and in less than a day to accomplish the same results as catalysts 1+3. The novel catalyst systems minimize thermodynamic equilibration of alkene isomers, so that the trans-2-alkenes of both non-functionalized and functionalized alkenes can be generated.