Genomatica Inc., a San Diego company that delivers new manufacturing processes to enable its partners to produce intermediate and basic chemicals from renewable raw materials, has raised $41.5 million in a Series D round of preferred stock financing.

New investor and partner Versalis, an Italian chemical company, participated in the round along with existing investors Alloy Ventures, Draper Fisher Jurvetson, Mohr Davidow Ventures, TPG Biotech, VantagePoint Capital Partners and Waste Management.

“Genomatica has demonstrated superior abilities to develop economically attractive process technologies that can enable a new approach for our industry,” said Versalis CEO Daniele Ferrari.

Genomatica said the investment was made at a significant increase in valuation compared to a Series C-1 round of financing, which was announced in March 2011.

Genomatica also announced it has withdrawn the registration statement it filed with the U.S. Securities and Exchange Commission on Aug. 23, 2011, relating to a proposed initial public offering of shares of its common stock.

“After evaluating all of our financing options, we determined that this private financing was the most attractive option for Genomatica and in the best interest of our shareholders,” said Genomatica CEO Christophe Schilling in a statement.