Amendment No. 1 to the Subordinated Convertible Note Purchase Agreement



 Exhibit 10.41 
 AMENDMENT NO. 1 TO 
 SUBORDINATED CONVERTIBLE NOTE PURCHASE AGREEMENT

 This Amendment No. 1 to the Subordinated Convertible Note Purchase Agreement (this
“Amendment”) is made and entered into as of June 1, 2010, by and among Mascoma Corporation, a Delaware corporation (the “Company”), and the Purchasers parties hereto. Capitalized terms used
herein, but not otherwise defined herein, shall have the meanings ascribed to such terms in the Note Purchase Agreement (as defined below). 
 WHEREAS, the Company and certain Purchasers are parties to that certain Subordinated Convertible Note Purchase Agreement, dated as of April 7, 2010 (the “Note Purchase
Agreement”); 
 WHEREAS, the Company and the Purchasers whose signatures are affixed below desire to
amend the Note Purchase Agreement to modify the process for selling certain of the Notes; 
 WHEREAS, pursuant to
Section 5.02 of the Note Purchase Agreement, any provision of the Note Purchase Agreement can be amended if the Company shall obtain consent thereto in writing from the Purchasers holding at least 66 2/3% of the principal outstanding under the
then outstanding Notes (the “Requisite Purchasers”); and 
 WHEREAS, the undersigned
Purchasers represent the Requisite Purchasers. 
 NOW THEREFORE, the parties hereby agree as follows: 

 

	 	1.	Section 1.02(b) of the Note Purchase Agreement shall be amended and restated in its entirety as set forth below: 


“(b) The Follow-On Closing. Following the Initial Closing, the Company will offer up to $1,419,000 total
principal amount of Notes, on a pro rata basis (based on shares of the Company’s Common Stock, par value $0.001 per share (the “Common Stock”) issuable upon conversion of the Preferred Stock (as defined below) held by
such holders), to the holders of the Company’s Preferred Stock who are not Initial Purchasers (the “Other Investors”). Any Other Investor who commits to purchase Notes shall execute an Additional Purchaser signature page
to this Agreement, in substantially the form attached hereto as Schedule A, and shall thereafter be bound to this Agreement as an Additional Purchaser, and Exhibit B attached hereto shall be updated to include the principal amount of
Notes that each Additional Purchaser has committed to purchasing. Forty percent (40%) of each Additional Purchaser’s commitment shall be funded at the Follow- On Closing (as defined below) and the remaining sixty percent (60%) shall
be funded at the Second Closing (as defined below). The initial purchase and sale of the Notes to the Additional Purchasers shall take place at a closing (the “Follow-On Closing”) to be held no later than sixty (60) days
after the Initial Closing.” 







 Any Notes offered to the Other Investors that are not purchased by the Other Investors at
the Follow-On Closing (the “Additional Follow-On Notes”) may be offered and sold by the Company in accordance with Section 1.02(c) below.” 

 

	 	2.	Section 1.02(c) of the Note Purchase Agreement shall be amended and restated in its entirety as set forth below: 


“(c) The Second Closing. After the Initial Closing and the Follow-On Closing, the Company shall sell, and the Purchasers shall
purchase, Notes in the principal amounts set forth opposite each Purchaser’s name on Exhibit A (for Initial Purchasers) or Exhibit B (for Additional Purchasers) under the heading “Principal Amount of Notes to Be Purchased at
the Second Closing.” Such purchase and sale shall take place at a closing (the “Second Closing,” and together with the Initial Closing, the Follow-On Closing and the Final Closing (as defined below), the
“Closings” and each individually a “Closing”) to be held no sooner than two (2) days and no later than ten (10) days following the approval by (A) the Board of Directors of the Company
and (B) the Purchasers holding at least sixty-six and two-thirds percent (66 2/3%) of the principal amount of the outstanding Notes then held by all Purchasers of (i) a business plan and strategy for monetization of the Company’s corn
CBP business and (ii) a plan for near- term acquisition opportunities for the Company (the “Second Closing Approval”); provided that if the Second Closing Approval does not occur on or before June 15, 2010,
the Purchasers shall be relieved of their obligation to purchase any additional Notes hereunder. Notwithstanding the foregoing, if a Purchaser (an “Opting Out Purchaser”) obligated to purchase a Note at the Second Closing
chooses not to purchase such Note at the Second Closing, such Opting Out Purchaser shall be relieved of its obligation to purchase such Note, but such Opting Out Purchaser shall be subject to the Mandatory Conversion described in
Section 1.02(e). Each Purchaser shall give the Company notice, at least two (2) days prior to the Second Closing, if such Purchaser shall be an Opting Out Purchaser. 
 The Additional Follow-On Notes and any Notes not purchased at the Second Closing by Opting Out Purchasers (the “Additional Opt Out Notes,” and together with the Additional
Follow-On Notes, the “Additional Notes”) may be offered by the Company to Purchasers who have funded or committed to fund their entire pro rata portion of Notes (collectively, the “Participating
Purchasers”) on a pro rata basis to the Notes purchased by all Participating Purchasers. If and to the extent that the Participating Purchasers do not agree to purchase all Additional Notes, the Company may, in its sole discretion,
apportion and offer the Additional Notes as to which one or more Participating Purchasers has declined the Company’s offer to purchase to one or more of the Participating Purchasers. Upon the acceptance by any Participating Purchaser of the
Company’s offer to purchase Additional Notes, the principal amount of Notes set forth opposite such Purchaser’s name under the column “Principal Amount of Notes Purchased at the Second Closing” or “Principal Amount of
Additional Notes Purchased at the Final Closing” on Exhibit A or Exhibit B, as the case may be, shall be increased by the 

  
 2 








 
Company in an amount equal to the principal amount of the Additional Notes agreed to be purchased by such Participating Purchaser. The purchase and sale of the Additional Notes shall take place
either at the Second Closing or at a final closing to be held within ten (10) business days following the Second Closing (the “Final Closing”), as determined by the Company.” 

 

	 	3.	Except as amended hereby, the remainder of the Note Purchase Agreement shall remain in full force and effect. 


 

	 	4.	This Amendment shall be governed by, and construed and enforced in accordance with, the substantive laws of the State of Delaware without regard to its principles of
conflicts of laws. 

  

	 	5.	This Amendment may be executed in any number of counterparts, each of which shall be deemed an original, but all of which taken together shall constitute one and the
same instrument, and any of the parties hereto may execute this Agreement by signing any such counterpart. This Amendment may be executed and delivered by facsimile, or by e-mail in portable document format (.pdf) and delivery of the signature page
by such method will be deemed to have the same effect as if the original signature had been delivered to the other parties. This Amendment shall take effect when executed by the Company and the Requisite Purchasers. 


[REMAINDER OF THIS PAGE INTENTIONALLY LEFT BLANK] 

  
 3 








 IN WITNESS WHEREOF, the parties hereto have executed this Amendment No. 1 to
Subordinated Convertible Note Purchase Agreement on the day, month and year first above written. 
  

			
	MASCOMA CORPORATION
		
	By:	 	  

		 	Name:
		 	Title:









 
	
	 /s/ R. Jeremy Grantham

	R. Jeremy Grantham


 Mascoma Corp. Amendment No 1 to Subordinated Convertible Note Purchase Agreement dated June 1, 2010








 
			
	 PINNACLE VENTURES II-A, L.P
 PINNACLE VENTURES II-B, L.P.
 PINNACLE VENTURES II-C, L.P.

PINNACLE VENTURES II-R, L.P.
 PINNACLE
VENTURES EQUITY FUND I, L.P.

	PINNACLE VENTURES EQUITY FUND I-O, L.P.
	PINNACLE VENTURES EQUITY FUND I AFFILIATES, L.P.
	
	 By Pinnacle Ventures Equity Management I, L.L.C.,
 its general partner

		
	By:	 	 /s/ Robert N. Savoie

	Name:	 	Robert N. Savoie
	Title:	 	Chief Financial Officer









 
			
	ATLAS VENTURE FUND VII, L.P.
	By:	 	 Atlas Venture Associates VII, L.P.,
Its General Partner

	By:	 	 Atlas Venture Associates VII, Inc.,
Its General Partner

		
	By:	 	 /s/ Kristen Laguerre

	Name:	 	Kristen Laguerre
	Title:	 	VP









 
					
	GENERAL MOTORS HOLDINGS LLC
		
	By:	 	 /s/ Rajesh Yadava

		 	Name:	 	 Rajesh Yadava 

		 	Title:	 	Director of Business Development, Treasurer’s Office









 
			
	FLAGSHIP VENTURES FUND 2004, L.P.
	
	 By: its General Partner
 Flagship Ventures General Partner LLC

		
	By:	 	 /s/ Noubar B. Afeyan

		 	Name:
		 	Title:









 
					
	 GENERAL CATALYST GROUP IV, L.P.
 By: General Catalyst Partners IV, L.P., its General Partner

	
	By: General Catalyst GP IV, LLC, General Partner
	By:	 	 /s/ William J. Fitzgerald

		 	Name:	 	William J. Fitzgerald
		 	Title:	 	Member and Chief Financial Officer
	
	 GC ENTREPRENEURS FUND IV, L.P.
 By: General Catalyst Partners IV, L.P., its General Partner

	
	By: General Catalyst GP IV, LLC, its General Partner
		
	By:	 	 /s/ William J. Fitzgerald

		 	Name:	 	William J. Fitzgerald
		 	Title:	 	Member and Chief Financial Officer









 
					
	KHOSLA VENTURES I, LP
	
	By: Khosla Ventures Associates I, LLC, a Delaware limited liability company and general partner of Khosla Ventures I, LP
		
	By:	 	 /s/ SAMIR KAUL

		 	Name:	 	SAMIR KAUL
		 	Title:	 	PARTNER









 
					
	KPCB HOLDINGS, INC., as nominee
		
	By:	 	 /s/ ERIC KELLER

		 	Name:	 	ERIC KELLER
		 	Title:	 	PRESIDENT









 
					
	BLUESTEM GROWTH & INCOME FUND III, LLC
	
	By: Bluestem Capital Company, LLC
		
	By:	 	 /s/ Steve Kirby

		 	Name:	 	Steve Kirby
		 	Title:	 	President









 
					
	BLUESTEM SELECT OPPORTUNITIES FUND, LLC
	
	By: Bluestem Capital Company, LLC
		
	By:	 	 /s/ Steve Kirby

		 	Name:	 	Steve Kirby
		 	Title:	 	President









 
					
	MPC INVESTMENT LLC
		
	By:	 	 /s/ Clifford C. Cook

		 	Name:	 	 Clifford C. Cook 

		 	Title:	 	Manager
			
		 		 	













 
					
	MALAYSIAN LIFE SCIENCES CAPITAL FUND
		
	By:	 	 /s/ ROGER WYSE

		 	Name:	 	ROGER WYSE
		 	Title:	 	CO-CHAIRMAN









 
					
	PIPER JAFFRAY & CO.
		
	By:	 	 /s/ Robert P. Rinek

		 	Name:	 	Robert P. Rinek
		 	Title:	 	Managing Director









 
	
	 /s/ David Mann

	David Mann









 
					
	CRM HOLDINGS, LLC
		
	By:	 	 /s/ Michael Ladiseh

		 	Name:	 	Michael Ladiseh
		 	Title:	 	Partner
		 		 	6/7/2010









 
			
	ATLAS VENTURE FUND VII, L.P.
	 By:
	 	 Atlas Venture Associates VII, L.P.,
Its General Partner

	By:	 	 Atlas Venture Associates VII, Inc.,
Its General Partner

		
	By:	 	 /s/ Kristen Laguerre

	Name:	 	Kristen Laguerre
	Title:	 	VP









 
	
	 /s/ Bruce A. Jamerson 6/9/10

	Bruce A. Jamerson









 
			
	VPVP CLEANTECH HOLDINGS 2006, L.L.C.
		
	By:	 	 VantagePoint Venture Partners 2006 (Q), L.P.,
 Its Sole Member

	By:	 	 VantagePoint Venture Associates 2006, L.L.C.,
 Its Managing Member

		
	By:	 	 /s/ Alan E. Salzman

	Name:	 	Alan E. Salzman
	Title:	 	Managing Member
	
	VANTAGEPOINT CLEANTECH PARTNERS, L.P.
		
	By:	 	 VantagePoint CleanTech Associates, L.L.C.,
 Its General Partner

		
	By:	 	 /s/ Alan E. Salzman

	Name:	 	Alan E. Salzman
	Title:	 	Managing Member









 
					
	FAGEN, INC.
		
	By:	 	 /s/ Ron Fagen

		 	Name:	 	Ron Fagen
		 	Title:	 	CEO & President









 
					
	STACK, LLC
		
	By:	 	 /s/ Fred M. Fehsenfeld, Jr.

		 	Name:	 	Fred M. Fehsenfeld, Jr.
		 	Title:	 	Chief Operating Officer