A well-known Silicon Valley investor with a penchant for green technology companies has raised more than $1 billion for two new venture funds.

Vinod Khosla, the California businessman who has spent hundreds of millions of his own money on clean-tech deals, said Khosla Ventures will fund start-ups that focus on clean energy, sustainability and information technology. It will make investments of up to $15 million from its main $800 million fund and offer seed money to the tune of $2 million to early-stage ideas from its smaller $275 million fund.

“It’s really geared toward science experiments,” said Khosla, the founder of Sun Microsystems. “The goal there is very much to take risks that nobody else will take.”

In trying economic times, it is certainly a lofty goal. The National Venture Capital Association said Khosla’s fund has amassed more capital than any other venture capital firm since 2007. It’s also the largest first-time fund since 1999.

And because of shrinking returns, investors have been favoring small funds and staying away from bigger, riskier deals with alternative energy companies. Venture capitalists put $513 million into 83 clean-tech companies in the first half of 2009, down from $2 billion into 139 companies last year, according to PricewaterhouseCoopers.

But it’s just the latest endeavor for Khosla, a prominent entrepreneur from India who dreamt of starting his own technology company when he was 16 and first heard about Intel starting up.

At age 20, Khosla tried – unsuccessfully – to start a soymilk company geared toward customers in India who lacked refrigerators. But by the time he earned a business degree at Stanford University in 1980, he was well on his way. He started Sun Microsystems in 1982 and later joined top venture firm Kleiner Perkins Caufield & Byers.

In 2004, Khosla left the firm to spend more time with his children and to take on “science experiments,” including “social impact” ventures. In the five years since, he has invested more than $400 million of his own money into companies that reduce dependence on coal and oil or increase energy efficiency.

One of his investments is a company that’s working on compressor-free air conditioners, while another, Calera, makes “green cement for a blue planet” by taking the carbon dioxide from burning coal, driving it through water, converting it to carbonate and producing cement.

In addition to raising $1.1 billion, Khosla Ventures also brought in two new partners, including Gideon Yu, the former CFO at Facebook and YouTube, and James Kim, who ran the clean-tech investing at CMEA Capital and GE Capital.

Bolstered by the partners’ own investment of roughly $100 million, the California Public Employees Retirement System, or CalPERS, invested $60 million in the seed fund and $200 million in the main fund.

For Khosla, it’s “really about reinventing the infrastructure of society, which is the only way we’ll get the carbon footprint down,” he said. “We’re not afraid to fail.”

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