Mascoma Corp Sample Contracts

—] Shares MASCOMA CORPORATION [—] SHARES OF COMMON STOCK, PAR VALUE $0.001 PER SHARE UNDERWRITING AGREEMENT
Underwriting Agreement • March 16th, 2012 • Mascoma Corp • Industrial organic chemicals • New York
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Form of Indemnification Agreement INDEMNITY AGREEMENT
Indemnity Agreement • December 9th, 2011 • Mascoma Corp • Industrial organic chemicals • Delaware

This Indemnity Agreement (this “Agreement”), dated as of , , is made by and between Mascoma Corporation, a Delaware corporation (the “Company”), and , a director and/or officer of the Company (the “Indemnitee”).

Contract
Mascoma Corp • December 9th, 2011 • Industrial organic chemicals • California

THIS WARRANT HAS NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED OR ANY STATE SECURITIES LAWS. NO SALE OR DISPOSITION MAY BE EFFECTED WITHOUT (i) EFFECTIVE REGISTRATION STATEMENTS RELATED THERETO, (ii) AN OPINION OF COUNSEL OR OTHER EVIDENCE, REASONABLY SATISFACTORY TO THE COMPANY, THAT SUCH REGISTRATIONS ARE NOT REQUIRED, (iii) RECEIPT OF NO-ACTION LETTERS FROM THE APPROPRIATE GOVERNMENTAL AUTHORITIES, OR (iv) OTHERWISE COMPLYING WITH THE PROVISIONS OF SECTION 8 OF THIS WARRANT.

LOAN AND SECURITY AGREEMENT
Loan and Security Agreement • December 9th, 2011 • Mascoma Corp • Industrial organic chemicals • California

This LOAN AND SECURITY AGREEMENT, dated as of October 6, 2006 (this “Loan Agreement”), is entered by and between MASCOMA CORPORATION, a Delaware corporation (“Borrower”); and PINNACLE VENTURES, L.L.C. as agent (“Agent”) for the lenders identified on Schedule 1 hereto (such lenders, together with their respective successors and assigns are referred to hereinafter each individually as a “Lender” and collectively as the “Lenders”), and the Lenders. Capitalized terms used and not otherwise defined in this Loan Agreement shall have the respective meanings given to such terms in Article 10.

MASCOMA CORPORATION WARRANT TO PURCHASE COMMON STOCK
Mascoma Corp • December 9th, 2011 • Industrial organic chemicals • Delaware

This Warrant is being issued pursuant to the terms of the Share Purchase Agreement, dated of even date herewith, by and among the Company and the other parties named therein (the “Purchase Agreement”).

Contract
Mascoma Corp • December 9th, 2011 • Industrial organic chemicals • California

THIS WARRANT HAS NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED OR ANY STATE SECURITIES LAWS. NO SALE OR DISPOSITION MAY BE EFFECTED WITHOUT (i) EFFECTIVE REGISTRATION STATEMENTS RELATED THERETO, (ii) AN OPINION OF COUNSEL OR OTHER EVIDENCE, REASONABLY SATISFACTORY TO THE COMPANY, THAT SUCH REGISTRATIONS ARE NOT REQUIRED, (iii) RECEIPT OF NO-ACTION LETTERS FROM THE APPROPRIATE GOVERNMENTAL AUTHORITIES, OR (iv) OTHERWISE COMPLYING WITH THE PROVISIONS OF SECTION 8 OF THIS WARRANT.

WARRANT PURCHASE AGREEMENT
Warrant Purchase Agreement • December 9th, 2011 • Mascoma Corp • Industrial organic chemicals • California

This Warrant Purchase Agreement (this “Agreement”) is made and entered into as of June 1, 2011 by and between MASCOMA CORPORATION, a Delaware corporation (the “Company”), and Pinnacle Ventures III Equity Holdings, L.L.C., a Delaware limited liability company (“Purchaser”).

WARRANT PURCHASE AGREEMENT
Warrant Purchase Agreement • December 9th, 2011 • Mascoma Corp • Industrial organic chemicals • California

This Warrant Purchase Agreement (this “Agreement”) is made and entered into as of February 5, 2008 by and between MASCOMA CORPORATION, a Delaware corporation (the “Company”), and Pinnacle Ventures II Equity Holdings, L.L.C., a Delaware limited liability company (“Purchaser”).

AMENDMENT NO. 2 TO THIRD AMENDED AND RESTATED REGISTRATION RIGHTS AGREEMENT
Registration Rights Agreement • December 9th, 2011 • Mascoma Corp • Industrial organic chemicals • Delaware

This Amendment No. 2 (this “Amendment”) to that certain Third Amended and Restated Registration Rights Agreement, dated as of August 31, 2010, by and among Mascoma Corporation, a Delaware corporation (the “Corporation”), and the Investors and Key Stockholders named therein, as amended (the “Registration Rights Agreement”), is made as of June 1, 2011, by and among the Corporation, Pinnacle Ventures, L.L.C., a Delaware limited liability company (“Pinnacle”), and the holders of Registrable Securities (as defined in the Registration Rights Agreement) listed on the signature pages hereto (“Rights Holders”).

CONSULTING AGREEMENT
Consulting Agreement • December 9th, 2011 • Mascoma Corp • Industrial organic chemicals • Massachusetts

This Consulting Agreement dated as of March 10, 2006 (this “Agreement”) is made by and between Lee R. Lynd (the “Consultant”) and Mascoma Corporation, a Delaware corporation (the “Company”).

DEVELOPMENT AND LICENSE AGREEMENT
Development and License Agreement • March 16th, 2012 • Mascoma Corp • Industrial organic chemicals • Delaware

THIS DEVELOPMENT AND LICENSE AGREEMENT (this “Agreement”) entered into on December 8, 2011 (the “Effective Date”), is by and between MASCOMA CORPORATION 67 Etna Road, Suite 300, Lebanon, NH 03766 (“Mascoma”), and LALLEMAND SPECIALTIES, INC., 6120 West Douglas Avenue, Milwaukee, WI 53218, doing business as Lallemand Ethanol Technology (“Lallemand”).

MASCOMA - DARTMOUTH EXCLUSIVE LICENSE AGREEMENT
Mascoma - Dartmouth Exclusive License Agreement • March 16th, 2012 • Mascoma Corp • Industrial organic chemicals • New Hampshire

This Agreement, effective this 10th day of July 2006, between the TRUSTEES OF DARTMOUTH COLLEGE, a non-profit educational and research institution existing under the laws of the State of New Hampshire, and being located at Hanover, New Hampshire 03755, hereinafter called Dartmouth, and MASCOMA CORPORATION, a corporation of the State of Delaware, with a principal place of business at 161 First Street, 2nd Floor East, Cambridge, Massachusetts 02142, hereinafter called Company.

KINROSS CELLULOSIC ETHANOL LLC LIMITED LIABILITY COMPANY AGREEMENT DATED AS OF DECEMBER 2, 2011
Limited Liability Company Agreement • March 16th, 2012 • Mascoma Corp • Industrial organic chemicals • Delaware

THIS LIMITED LIABILITY COMPANY AGREEMENT is made and entered into by and among the Company and the Members as of December 2, 2011 (the “Effective Date”).

COLLABORATION AGREEMENT BY AND BETWEEN MASCOMA CORPORATION AND AND FRONTIER RENEWABLE RESOURCES, LLC
Collaboration Agreement • March 16th, 2012 • Mascoma Corp • Industrial organic chemicals • Delaware

This Collaboration Agreement is made this 15th day of December, 2008 (the “Effective Date”) by and among MASCOMA CORPORATION, a Delaware corporation (“Mascoma”), J.M. LONGYEAR, L.L.C., a Michigan limited liability company (“Longyear”), and Frontier Renewable Resources, LLC, a Delaware limited liability company (the “Company” or “Frontier”). Each of Mascoma and Longyear are sometimes referred to herein as a “Member” or collectively as the “Members”. The Members and the Company shall be referred to separately as a “Party”, and collectively, the “Parties”. Capitalized terms used by not defined herein shall have the meanings ascribed to such terms in the Operating Agreement (as defined below).

LIMITED LIABILITY COMPANY OPERATING AGREEMENT OF FRONTIER RENEWABLE RESOURCES, LLC
Limited Liability Company Operating Agreement • March 16th, 2012 • Mascoma Corp • Industrial organic chemicals • Delaware

THIS LIMITED LIABILITY COMPANY OPERATING AGREEMENT (the “Agreement”), dated as of December 15, 2008, is entered into by and among FRONTIER RENEWABLE RESOURCES, LLC (the “Company”); MASCOMA CORPORATION, a corporation organized and existing under the laws of the State of Delaware (“Mascoma”); and J.M. LONGYEAR, L.L.C., a Michigan limited liability company being organized hereby under the laws of the State of Michigan (“Longyear”). Mascoma and Longyear are also hereinafter sometimes individually referred to as the “Member” or collectively as the “Members.”

TRANSITION AND SPECIAL CONSULTING AGREEMENT
Transition and Special Consulting Agreement • December 9th, 2011 • Mascoma Corp • Industrial organic chemicals • Massachusetts

provision shall be severed from the remainder of this Release. In the event of such severance, the remaining provisions shall be binding and enforceable.

Biorefining Commercialization and Market Development Program Grant Agreement
Grant Agreement • March 16th, 2012 • Mascoma Corp • Industrial organic chemicals • Alberta

The Province developed the Biorefining Commercialization and Market Development Program (the “Program”) as part of its nine point “Bioenergy Plan”, to develop, expand and strengthen Alberta’s biodiesel, biogas (methane), ethanol and other new generation fuel production capacity in response to market demands. The Program is designed to stimulate investment in the bio-energy sector in Alberta through construction of ethanol, biodiesel and biogas (methane) processing facilities in Alberta.

AMENDMENT NO. 1 TO LOAN AND SECURITY AGREEMENT
Loan and Security Agreement • December 9th, 2011 • Mascoma Corp • Industrial organic chemicals • California

This AMENDMENT NO. 1 TO LOAN AND SECURITY AGREEMENT (this “Amendment”), dated as of December 30, 2008, is entered into by and among MASCOMA CORPORATION, a Delaware corporation (the “Borrower”), Pinnacle Ventures, L.L.C. as agent (“Agent”) for each of the lenders that is a signatory to this Amendment (individually, a “Lender” and collectively, the “Lenders”), and the Lenders.

CONTRIBUTION AGREEMENT
Technology License and Supply Agreement • March 16th, 2012 • Mascoma Corp • Industrial organic chemicals • Delaware

THIS CONTRIBUTION AGREEMENT is made and entered into as of December 2, 2011, by and among Frontier Renewable Resources, LLC, a Delaware limited liability company (the “Frontier Member”), Diamond Alternative Energy, LLC, a Delaware limited liability company (the “Valero Member”), Mascoma Corporation, a Delaware corporation (“Mascoma”), Valero Services, Inc., a Delaware corporation (“Valero Services”), Valero Marketing and Supply Company, a Delaware corporation (“VMSC”), JML Heirs, LLC, a Michigan limited liability company (“JML”), and Kinross Cellulosic Ethanol LLC, a Delaware limited liability company (the “Company”).

SUBORDINATED CONVERTIBLE PROMISSORY NOTE AND WARRANT PURCHASE AGREEMENT
Convertible Promissory Note and Warrant Purchase Agreement • December 9th, 2011 • Mascoma Corp • Industrial organic chemicals • Delaware

This SUBORDINATED CONVERTIBLE NOTE AND WARRANT PURCHASE AGREEMENT (the “Agreement”) is made and entered into as of August 5, 2011, by and among Mascoma Corporation, a Delaware corporation (the “Company”), the initial purchasers listed on Exhibit A attached hereto (each an “Initial Purchaser” and collectively the “Initial Purchasers”) and the additional purchasers listed on Exhibit B attached hereto (each an “Additional Purchaser” and collectively the “Additional Purchasers”). The Initial Purchasers and the Additional Purchasers are referred to herein as the “Purchasers,” and each individually a “Purchaser.” Capitalized terms used herein but not defined herein shall have the meanings ascribed to them in the Notes (as defined below).

Contract
Grant Agreement • March 16th, 2012 • Mascoma Corp • Industrial organic chemicals • Michigan

PORTIONS OF THIS EXHIBIT WERE OMITTED AND HAVE BEEN FILED SEPARATELY WITH THE SECRETARY OF THE COMMISSION PURSUANT TO AN APPLICATION FOR CONFIDENTIAL TREATMENT UNDER RULE 406 OF THE SECURITIES ACT; [***] DENOTES OMISSIONS.

Contract
Grant Agreement • December 9th, 2011 • Mascoma Corp • Industrial organic chemicals • Michigan

PORTIONS OF THIS EXHIBIT WERE OMITTED AND HAVE BEEN FILED SEPARATELY WITH THE SECRETARY OF THE COMMISSION PURSUANT TO AN APPLICATION FOR CONFIDENTIAL TREATMENT UNDER RULE 406 OF THE SECURITIES ACT; [***] DENOTES OMISSIONS.

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LIMITED LIABILITY COMPANY AGREEMENT OF FRONTIER KINROSS, LLC
Limited Liability Company Agreement • December 9th, 2011 • Mascoma Corp • Industrial organic chemicals • Delaware

THIS LIMITED LIABILITY COMPANY AGREEMENT (this “Agreement”) by the undersigned sole member (the “Member”) of Frontier Kinross, LLC, a Delaware limited liability company (the “Company”), is effective as of the date of formation of the Company.

MASTER COMMERCIAL COLLABORATION AGREEMENT
Master Commercial Collaboration Agreement • March 16th, 2012 • Mascoma Corp • Industrial organic chemicals • New York

This Master Commercial Collaboration Agreement (this “Agreement”), dated November 16th 2011, is between Valero Renewable Fuels Company LLC, having its principal place of business at One Valero Way, San Antonio, TX 78249-1616 (“VRF”) and Mascoma Corporation, having its principal place of business at 67 Etna Road, Suite 300, Lebanon, NH 03766 (“Mascoma”). VRF and Mascoma are sometimes herein collectively referred to as “Parties” and individually as a “Party”.

SUBORDINATED CONVERTIBLE NOTE PURCHASE AGREEMENT
Subordinated Convertible Note Purchase Agreement • December 9th, 2011 • Mascoma Corp • Industrial organic chemicals • Delaware

This SUBORDINATED CONVERTIBLE NOTE PURCHASE AGREEMENT (the “Agreement”) is made and entered into as of April 7, 2010, by and among Mascoma Corporation, a Delaware corporation (the “Company”), the initial purchasers listed on Exhibit A attached hereto (each an “Initial Purchaser” and collectively the “Initial Purchasers”) and the additional purchasers listed on Exhibit B attached hereto (each an “Additional Purchaser” and collectively the “Additional Purchasers”). The Initial Purchasers and the Additional Purchasers are referred to herein as the “Purchasers,” and each individually a “Purchaser.”

AMENDMENT NO. 1 TO THIRD AMENDED AND RESTATED REGISTRATION RIGHTS AGREEMENT
Registration Rights Agreement • December 9th, 2011 • Mascoma Corp • Industrial organic chemicals • Delaware

This Amendment No. 1 (this “Amendment”) to that certain Third Amended and Restated Registration Rights Agreement, dated as of August 31, 2010, by and among Mascoma Corporation, a Delaware corporation (the “Corporation”), and the Investors and Key Stockholders named therein (the “Registration Rights Agreement”), is made as of January 7, 2011, by and among the Corporation, Diamond Alternative Energy, LLC, a Delaware limited liability company (“Valero”), and the holders of Registrable Securities (as defined in the Registration Rights Agreement) listed on the signature pages hereto (“Rights Holders”).

FIRST AMENDMENT TO LIMITED LIABILITY COMPANY OPERATING AGREEMENT OF FRONTIER RENEWABLE RESOURCES, LLC
Access Agreement • December 9th, 2011 • Mascoma Corp • Industrial organic chemicals • Michigan

THIS FIRST AMENDMENT TO LIMITED LIABILITY COMPANY OPERATING AGREEMENT (the “Amendment Agreement”), is dated as of June __, 2010, is entered into by and among FRONTIER RENEWABLE RESOURCES, LLC (the “Company”); MASCOMA CORPORATION, a Delaware corporation (“Mascoma”); and J.M. LONGYEAR, L.L.C., a Michigan limited liability company (“Longyear”). (Mascoma and Longyear are also hereinafter sometimes individually referred to as the “Member” or collectively as the “Members.”)

CONTRIBUTION AGREEMENT
License and Supply Agreement • December 9th, 2011 • Mascoma Corp • Industrial organic chemicals • Delaware

THIS CONTRIBUTION AGREEMENT is made and entered into as of December 2, 2011, by and among Frontier Renewable Resources, LLC, a Delaware limited liability company (the “Frontier Member” ), Diamond Alternative Energy, LLC, a Delaware limited liability company (the “Valero Member” ), Mascoma Corporation, a Delaware corporation ( “Mascoma” ), Valero Services, Inc., a Delaware corporation ( “Valero Services” ), Valero Marketing and Supply Company, a Delaware corporation ( “VMSC” ), JML Heirs, LLC, a Michigan limited liability company ( “JML” ), and Kinross Cellulosic Ethanol LLC, a Delaware limited liability company (the “Company” ).

COLLABORATION AGREEMENT
Collaboration Agreement • December 9th, 2011 • Mascoma Corp • Industrial organic chemicals • New York

This Collaboration Agreement is entered into as of this 21st day of October, 2011 (the “Effective Date”) by and between ICM, Inc., a Kansas corporation with a principal address at P.O. Box 397, 310 N. First Street, Colwich, KS 67030-0397 (“ICM”) and Mascoma Corporation, a Delaware corporation with a principal address at 67 Etna Road. Suite 300, Lebanon, NH 03766 (“Mascoma”; together with ICM, the “Parties” and each a “Party”).

RESEARCH AGREEMENT Mascoma Corporation and Dartmouth College
Agreement • December 9th, 2011 • Mascoma Corp • Industrial organic chemicals • New Hampshire

This Agreement (“AGREEMENT”) is executed by and between Mascoma Corporation, a Delaware corporation, with a principal place of business at 1380 Soldiers Field Road, Boston, Massachusetts 02135 (hereinafter referred to as “MASCOMA”) and the Trustees of Dartmouth College, a non-profit educational institution existing under the laws of the State of New Hampshire, and being located at Hanover, New Hampshire 03755 (hereinafter referred to as “DARTMOUTH”).

AMENDMENT NO. 1 TO SUBORDINATED CONVERTIBLE NOTE PURCHASE AGREEMENT
Subordinated Convertible Note Purchase Agreement • December 9th, 2011 • Mascoma Corp • Industrial organic chemicals • Delaware

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).

MASCOMA CORPORATION THIRD AMENDED AND RESTATED REGISTRATION RIGHTS AGREEMENT
Registration Rights Agreement • December 9th, 2011 • Mascoma Corp • Industrial organic chemicals • Delaware

THIS THIRD AMENDED AND RESTATED REGISTRATION RIGHTS AGREEMENT is entered into as of the 31st day of August, 2010, by and among Mascoma Corporation, a Delaware corporation (the “Corporation”), with its principal place of business located at 67 Etna Road, Suite 300, Lebanon, New Hampshire 03766, the holders of the Corporation’s Series D Preferred Stock, par value $0.001 per share (the “Series D Preferred Stock”), Series A1 Preferred Stock, par value $0.001 per share (the “Series A1 Preferred Stock”), Series A Preferred Stock, par value $0.001 per share (the “Series A Preferred Stock”), Series B Preferred Stock, par value $0.001 per share (the “Series B Preferred Stock”), and Series C Preferred Stock, par value $0.001 per share (the “Series C Preferred Stock” and, together with Series A1 Preferred Stock, Series A Preferred Stock, Series B Preferred Stock and Series D Preferred Stock, the “Preferred Stock”), and, together with the holders of Preferred Stock being hereinafter referred to in

MASCOMA CORPORATION
Mascoma Corp • December 9th, 2011 • Industrial organic chemicals • Massachusetts

The purpose of this letter agreement (this “Letter Agreement”) is to confirm our understanding with respect to your continued service to Mascoma Corporation (the “Company”) following the expiration of that certain Transition and Special Consulting Agreement, dated as of August 17, 2009, by and between you and the Company (the “Transition Agreement”) on August 19, 2011 (the “Transition Agreement Expiration Date”).

EXECUTIVE EMPLOYMENT AGREEMENT
Employment Agreement • December 9th, 2011 • Mascoma Corp • Industrial organic chemicals • Ontario

WHEREAS the Executive has occupied the office of President and Chief Technology Officer of SunOpta BioProcess Inc. pursuant to an employment agreement dated June 8, 2007;

LIMITED LIABILITY COMPANY OPERATING AGREEMENT OF FRONTIER RENEWABLE RESOURCES, LLC
Limited Liability Company Operating Agreement • December 9th, 2011 • Mascoma Corp • Industrial organic chemicals • Delaware

THIS LIMITED LIABILITY COMPANY OPERATING AGREEMENT (the “Agreement”), dated as of December 15, 2008, is entered into by and among FRONTIER RENEWABLE RESOURCES, LLC (the “Company”); MASCOMA CORPORATION, a corporation organized and existing under the laws of the State of Delaware (“Mascoma”); and J.M. LONGYEAR, L.L.C., a Michigan limited liability company being organized hereby under the laws of the State of Michigan (“Longyear”). Mascoma and Longyear are also hereinafter sometimes individually referred to as the “Member” or collectively as the “Members.”

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