A few of the stocks I covered yesterday are still down — like EnerNOC, but that’s due to company-specific issues. Most are slightly up, though many didn’t return to the trading levels pre-market sell-off. Here’s a run down on where the stocks I covered yesterday are at this morning:

Solar

• Solar panel maker SunPower up 3.06 percent.
• Chinese solar panel maker Suntech rises 4.13 percent.
• Thin-film solar maker First Solar is still down .40 percent.

Biofuels

• Biofuel maker Gevo is back up 10.87 percent.
• Algae oil company Solazyme is up 3.07 percent.
• Biofuel maker KiOR is down even more: 3.50 percent.
• Biofuel maker Amyris is up 0.75 percent.

Electric car and batteries

• Lithium ion battery maker A123 Systems is up 11.70 percent.
• Electric car maker Tesla Motors is up 5.67 percent.
• Battery maker Ener1 is up 6.75 percent.

Smart grid

• Smart meter and network maker Itron is up 5.14 percent.
• Demand response company Comverge is down even more, by 1.38 percent.
• Demand response leader EnerNOC crashed even more, by 36.98 percent . (Yesterday’s market crash is combined with EnerNOC’s own weak earnings statement and a downgraded position to hold by a prominent analyst).
• Smart meter and network maker Echelon is back up by 5.51 percent.

Random:

• Car sharing company Zipcar is up 2.75 percent. It hasn’t fully recovered from yesterday.
• Clean Energy Fuels, which makes natural gas infrastructure for gas-powered cars, is still down by 5.80 percent.

Image courtesy of dizznbonn.

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Chesapeake’s first two investments include $150 million into natural gas vehicle fueling company Clean Energy Fuels, which if you remember counts T. Boone Pickens as a Director (he also founded the company that later turned into Clean Energy Fuels). The other investment is $155 million into stealthy biofuel company Sundrop Fuels, which gives Chesapeake a 50 percent stake in Sundrop.

One billion dollars dedicated to new natural gas tech could have a substantial influence on some of the biofuel, fuel cell, or natural gas vehicle startups out there. Fuel cells, like Bloom Energy’s, can use natural gas to make electricity; there’s a variety of biofuel firms that can use natural gas as a feedstock to convert into renewable fuels’ and there are a few auto makers that are looking to develop better natural gas cars and fueling infrastructure.

Strategic cleantech investing is one of the bright spots in the seemingly depressed greentech industry. Oil companies Exxon, Chevron, and BP have made minor investments in biofuel companies, oil refiner Valerohas made some more substantial bets as well, and chemical giant Dow has backed a variety of startups recently. GE and Intel Capital have been the more established investors in the cleantech space. And there’s always the group approach, which NRG Energy, ConocoPhillips have taken. A GM event launched an inaugural $100 million auto tech fund.

Corporations that have energy interests can use VC arms to find the latest innovative technology, and then either invest and buy the tech, or enter into exclusive commercialization deals. While a lot of these early companies are risky, from the corporate’s perspective the investment is often times relatively small compared to its massive balance sheet. Chesapeake’s investments are some of the bigger ones coming out of the gate from a new investor — often times several million dollars is more standard.

Image of natural gas car at LA Auto Show.

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VPG was founded in 2006 and has been supported by more than $10 million of investment from Clean Energy Fuels, a natural gas distribution company, as well as $10 million of Pickens’ own funds. In total VPG has raised at least $160 million in an equity financing round led by the investment group Perseus, which Clean Energy and Pickens also joined.

VPG, based in Miami, Fla., started integrating a natural gas model into its business plan when it linked up with Clean Energy Fuels, VPG chief executive David Schembri tells us. The connection between the car startup, Clean Energy Fuels and its investors is a tight little love triangle formed around interests in natural gas vehicles, with Perseus also having invested in Clean Energy Fuels.

The Loan

VPG’s DOE loan is meant to finance engineering and manufacturing costs associated with producing a compressed natural gas version of its base model vehicle, which runs on gasoline. However, as a spokesperson in the DOE loan office noted to us this week, the gasoline-powered model, called the MV-1, does not qualify as an advanced vehicle under the loan program requirements. Compared to gasoline and diesel vehicles, according to the DOE, natural gas vehicles “can produce significantly lower carbon monoxide, nitrogen oxide, nonmethane hydrocarbon, particulate matter and other toxic emissions, as well as greenhouse gas emissions.”

Under the program rules, ATVM-funded vehicle projects from new companies like VPG have to deliver fuel economy improvements of at least 25 percent over the average for vehicles with in the 2005 model year with “substantially similar attributes.” For the purpose of this calculation, the loan program compared VPG’s MV-1 to passenger vans, according to the DOE.

Schembri expects to begin producing the MV-1 in late January 2011 and begin shipping to customers by May 2011. VPG plans to contract manufacturing out to AM General, a company that once built Hummers for General Motors at its Mishawaka, Indiana plant and now makes Humvees for the U.S. military.

Americans with Disabilities Act

VPG claims its design is “the only light-duty vehicle to date that meets or exceeds the guidelines of the Americans with Disabilities Act.” It has an access ramp at the side door that can hold up to 1,200 pounds, a 36-inch entryway and seating capacity for six people, including a wheelchair passenger and an optional jumpseat.

According to Schembri, VPG’s genesis traces to fleet vehicle operators trying to find a simpler, lower cost way to meet rising municipal requirements for wheelchair accommodations in taxi fleets and paratransit service (the Americans with Disabilities Act, or ADA, requires transit agencies to provide paratransit services to people with disabilities who cannot use the mainline bus or rail service).

“Fleet operators looked around for choices,” and found none, said Schmebri. To this day, virtually all vehicles equipped for wheelchair access are relatively expensive after-market conversions. An operator presented the problem to some of the people that would later found VPG, according to Schembri, and together they came up with a scheme to engineer and build a vehicle from the get-go for wheelchair accessibility.

Since ADA passed in 1990, said Schembri, “we’ve seen advancements everywhere except factory-direct autos.” Yet there’s a sizable market opportunity: Schembri cited estimates that 4 million people use a wheelchair in the U.S. and 10 million people use a walker, crutch or cane.

Natural Gas Cars

As for natural gas models, they make up a small portion of the global auto market. The Wall Street Journal reported this week (citing statistics from the International Association for Natural Gas Vehicles) that 11.4 million natural gas-powered vehicles are in use around the world, with most of them found in Pakistan, Iran, Argentina, Brazil and India.

In the U.S., compressed natural gas cars numbered only 110,000 last year, accounting for only a fraction of a percent of all transportation fuel used for on-road vehicles. These cars make the most economic sense for high-mileage fleet customers, which typically have central refueling stations (natural gas fueling infrastructure is very limited) and can reap savings from the lower cost fuel.

VPG is targeting four market segments with its MV-1, including consumers, municipal paratransit service providers, commercial fleets (such as limos and delivery), and taxi fleets. For fleet operators, the natural gas model could offer something of a two-for-one deal, said Schembri, helping them to meet heightening requirements for alternative fuel vehicles as well as wheelchair accessibility without having to foot the bill for retrofits.

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Regardless, as of April 2, FuelMaker, which makes “Phill,” the residential natural gas vehicle fueller, says it has ceased operations and gone bankrupt (hat tip Autoblog Green and The Auto Channel). If you call the company’s mainline answering machine you can hear a short explanation of the bankruptcy proceedings. The Phill just never seemed to take off — FuelMaker was founded in 1989 and started selling Phill 6 years ago. The fueller compresses natural gas from home gas lines, takes about four hours to fill an empty tank after a 50-mile drive, and costs between $5,500 and $6,000.

T. Boone and Clean Energy Fuels, which distributes natural gas fuel, had been trying to buy FuelMaker for $17 million from Honda and the FuelMaker Trust. According to Clean Energy Fuels and a regulatory filing, it was actually Honda who killed the deal. The regulatory filing just says: “Honda delivered to us a notice that it intended to terminate the purchase agreement; and, after subsequent discussions, on October 15, 2008, we and Honda mutually agreed to terminate the purchase agreement in accordance with its terms.” Clean Energy Fuel’s CEO Andrew Littlefair told us that the deal to buy FuelMaker from Honda fell through because Honda couldn’t provide financials in time, so Clean Energy Fuels just couldn’t legally buy it. The stalled deal was also holding up the company’s ability to raise its needed funds, said Littlefar, so had to be ended.

Honda had clearly been trying to sell the company for awhile. One of the biggest problems with the business model for Phill is that there’s very few natural gas vehicles for consumers on the market. The Honda Civic GX is about the only consumer natural gas car around and can be bought for $24,590 in select locations in California and New York. Bottom line: no cars out there to fill with natural gas, no reason for anyone to use a home gas fuelling system . . . no good reason to buy Phill.

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The company needs money due to the fact that it has been investing in various new businesses, including development of a natural gas vehicle, and a landfill gas waste project. The company also needs the money because, according to its earnings, it had a net loss of $10.64 million for the three months that ended September 30, compared to a net loss of $1.5 million for the third quarter of 2007. That’s a drop of more than 85 percent. Clean Energy’s revenues were more positive, however: Revenues for the third quarter of 2008 rose 21 percent to $35.3 million, up from $29.2 million for the third quarter of 2007.

We’ve also been wondering if the financial crisis was one of the reasons why Clean Energy’s deal to buy the residential natural gas vehicle refueler FuelMaker fell through in October. But Littlefair tells us the deal to buy FuelMaker from Honda fell through because Honda couldn’t provide financials in time, so Clean Energy Fuels just couldn’t legally buy it. The stalled deal was also holding up the company’s ability to raise its needed funds, said Littlefar, so had to be ended. Littlefair says Clean Energy Fuels is still interested in buying into the home distribution market — and potentially even in a future deal with FuelMaker.

In addition to losing the FuelMaker deal, Clean Energy suffered another setback this month. Voters of California rejected Prop 10, the California Renewable Energy and Clean Alternative Fuel Act, which Clean Energy Fuels had been backing and from which it would have benefited. In Clean Energy Fuel’s second quarter earnings it said it had increased its expenses on advertising by $2 million to support the California clean alternative fuel proposition, saying that the Alternative Fuels Act represented “a significant opportunity for our business.” Well, better luck in the next ballot box.

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In a blog post, David Drummond, Google’s chief legal officer, announced today that the company is withdrawing from the so-called Yahoo-Google advertising partnership, mostly because it was getting too much scrutiny from the federal government.

However, after four months of review, including discussions of various possible changes to the agreement, it’s clear that government regulators and some advertisers continue to have concerns about the agreement. Pressing ahead risked not only a protracted legal battle but also damage to relationships with valued partners. That wouldn’t have been in the long-term interests of Google or our users, so we have decided to end the agreement.

Despite those innocent-sounding words, deep down Google has to be secretly rejoicing over freezing Yahoo into inactivity. Did anyone actually believe that this deal was going to sail through? I sure didn’t. But apparently, in their desire to save themselves from Microsoft, Yahoo forgot that the guys in Mountain View, Calif., only play hardball.

At the time of the deal, I pointed out that, “[T]he U.S. government investigation is going to entangle Yahoo in underwater weeds of uncertainty. Google, on the other hand, will be victorious in defeat — they would have frozen Yahoo into inaction for awhile.” Yahoo “is shooting itself in the face with this deal,” I said then, likening the deal to knowing that “your spouse is going to divorce you while you’re standing in the aisle, waiting for the priest.”

Where does it leave Yahoo? That answer will come in a later after I return from the Web 2.0 conference.

Update: Statement from US Department of Justice:

Yahoo! Inc. and Google Inc. abandoned their advertising agreement after the Department of Justice informed the companies that it would file an antitrust lawsuit to block the implementation of the agreement. The Department said that, if implemented, the agreement between these two companies accounting for 90 percent or more of each relevant market would likely harm competition in the markets for Internet search advertising and Internet search syndication.

“The companies’ decision to abandon their agreement eliminates the competitive concerns identified during our investigation and eliminates the need to file an enforcement action,” said Thomas O. Barnett, Assistant Attorney General in charge of the Department’s Antitrust Division. “The arrangement likely would have denied consumers the benefits of competition –lower prices, better service and greater innovation.”

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There were few details given in the announcement as to why Honda and Clean Energy Fuels changed their minds, and we’re still waiting to hear back from the companies. But in the regulatory filing it sounds like Honda was actually the initiator of ending the agreement. In the filing Clean Energy Fuels says both companies had the right to terminate the purchase agreement if it did not close on or before Oct. 3, and this didn’t happen due to the fact that the sellers (Honda and Fuelmaker) were unable to deliver audited financial statements for FuelMaker’s parent company, a subsidiary of Honda, by that date. Clean Energy Fuels says it continued to negotiate but that on Oct. 13, 2008:

Honda delivered to us a notice that it intended to terminate the purchase agreement; and, after subsequent discussions, on October 15, 2008, we and Honda mutually agreed to terminate the purchase agreement in accordance with its terms.

That’s all we know, but the auto industry definitely has been having a hard time as of late. We talked briefly with FuelMaker President John Lyon and he referred us to Honda and Clean Energy Fuels for why the deal fell through.

Founded in 1989 and based in Toronto, FuelMaker manufactures natural-gas refueling appliances for industrial fleets, as well as a home consumer product called the Phill. Announced six years ago, the Phill compresses natural gas from home gas lines for vehicle fueling; it takes about four hours to fill an empty tank after a 50-mile drive. While it costs between $5,500 and $6,000 (there’s a possible tax rebate of $1,000 or so), Picken’s plan to power U.S. vehicles with natural gas could have used the Phill to help break the home distribution bottleneck.

But it looks like Clean Energy Fuel’s role in spearheading natural gas vehicle stations in our homes will just have to wait. FuelMaker was just one of Clean Energy Fuel’s planned acquisitions and investments. Earlier this year Clean Energy Fuels said it would purchase Dallas Clean Energy (DCE), owner of the McCommas Bluff landfill gas processing plant, for $19.1 million, and also agreed to co-invest $10 million (and another $10 million from Pickens) in the creation of a natural gas vehicle. The company’s stock (CLNE) was trading at $9.44 as of this writing, down from nearly $20 in early September.

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CleanScapes was founded over a decade ago by entrepreneur Chris Martin, who says in the release this morning that the new natural gas powered garbage trucks will be used mostly for residential collections, which will reduce both emissions and noise in populated areas. CleanScapes collects trash several times a day, picking up its color-coded bags for garbage, recycling and compost. The company also advocates trash reduction and is expanding into Portland and San Francisco.

It might not be a massive win for Clean Energy Fuels, but cozying up with city contractors is a solid way to get a natural gas pump built. San Francisco and San Jose’s mayors have both pushed for greener city fleets as a way to provide business for new cleantech companies. And while there are only about 1,100 natural-gas fueling stations in the U.S., according to Natural Gas Vehicles for America, the more pumps the better for Clean Energy Fuels to get natural gas into more fuel tanks.

Recently, Clean Energy Fuels has also taken a very aggressive approach to building out its business across the natural gas vehicle world. Earlier this month the company said it plans to acquire FuelMaker, makers of the home consumer natural gas refueller “The Phill,” from American Honda Corp. and the FuelMaker Trust for $17 million in cash. Previously the company said it had purchased Dallas Clean Energy (DCE), owner of the McCommas Bluff landfill gas processing plant, which the firms claim is the third largest landfill gas operation in the U.S, for $19.1 million. And earlier Clean Energy Fuels said it had joined with investment group Perseus and T. Boone Pickens to support the creation of a natural gas vehicle with investment to the tune of $160 million.

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The Phill, which was unveiled by Honda and FuelMaker in 2002, compresses natural gas from home gas lines, takes about four hours to fill an empty tank after a 50-mile drive, uses 800 watts, and weighs about 100 lbs. The biggest barrier to consumers buying the Phill is its price tag — we called the customer service line and the representative said we could get the Phill for between $5,500 and $6,000, including installation ($1,500) and shipping ($200). The representative said we were also eligible for a tax rebate of $1,000, or 30 percent of the cost.

In European countries like France, Italy, Switzerland, Poland, Finland, the Netherlands and Belgium, as well as in China, consumers can get the Phill through utility gas providers. In the U.S., you can buy the Phill directly in certain states. The device is meant to be installed in a garage or outside and in an installer needs to come to your house to pre-approve that your gas and electrical system is compatible.

Perhaps with Clean Energy Fuels, and Picken’s publicity, behind the wheel of the Phill, the device can get more distribution and awareness. We can’t imagine that many have been sold-to-date, given there’s still few natural gas vehicles on road. But then again former owner Honda has bigger pockets, and one of the most well known consumer natural gas cars out there — the Honda Civic GX, which costs $24,590, is sold in California and New York and has a 170-mile fuel range.

Clean Energy Fuels, despite a lack of profits, has taken an acquisition strategy to its growth. Last month the company said it had purchased Dallas Clean Energy (DCE) for $19.1 million. DCE is the owner of the McCommas Bluff landfill gas processing plant, which the firms claim is the third largest landfill gas operation in the U.S. Then earlier in August, Clean Energy Fuels, said it had joined with the investment group Perseus, and T. Boone Pickens to support the creation of a natural gas vehicle to the tune of $160 million. Clean Energy Fuels and Pickens plan to each commit $10 million, and Perseus is led the investment; the Vehicle Production Group will build the vehicle.

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While a Pelosi spokesperson insists to the WSJ that the holding “does not raise any direct conflict-of-interest issues” Pelosi has been a supporter of legislation that would benefit increased use of natural gas. But the real question would be, has Pelosi been an advocate of California’s Prop 10? The ballot measure is backed by Pickens and would give thousands of dollars in rebates to natural gas vehicle buyers, as well as spending on R&D, and supposedly cost California $9.8 billion over 30 years. We haven’t heard her publicly backing Prop 10, and you can guess if she hasn’t yet, she definitely isn’t going to now.

Pelosi’s shares represent less than 1 percent of the couple’s assets, which the WSJ says are in the range of $15 million and $52 million. Clean Energy Fuels (CLNE) shares rose at the end of last year and were worth as much as $20.64 in October, boosting Pelosi’s investment significantly, but prices have since fallen. The stock was trading at $14.32 this morning.

The Pickens-Pelosi link is also indicative of the changing view of Pickens in the democratic camp now that Pickens has turned green. Pickens, who helped fund the Swift Boat Veterans for Truth campaign that wounded Democratic Presidential candidate John Kerry’s campaign, was a keynote speaker at the National Clean Energy Summit last week organized by Nevada Senator, democrat Harry Reid. The summit was largely made up by democratic speakers (and likely attendees) and Pickens was frequently lauded throughout as an important figure behind clean energy.

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