Document:

EX-4.1

 Exhibit 4.1 

FIRST SUPPLEMENTAL INDENTURE 

This FIRST SUPPLEMENTAL INDENTURE (this “First Supplemental Indenture”), dated as of July 31, 2014, among Gevo, Inc., a
company duly incorporated and existing under the laws of Delaware, United States of America, and having its principal executive office at 345 Inverness Drive South, Building C, Suite 310, Englewood, CO 80112 as Issuer (the
“Company”), the guarantors listed on the signature page hereof (each, a “Guarantor” and, collectively, the “Guarantors”), Wilmington Savings Fund Society, FSB, as Trustee (in such capacity, the
“Trustee”), and WB Gevo, Ltd., as the holder of 100% of the aggregate principal amount of the outstanding Notes and the “Requisite Holder” under the Indenture (as defined below) (the “Requisite Holder”).
Capitalized terms used herein without definition have the meanings given in the Indenture (as defined below). 
 RECITALS 

WHEREAS, the Company, Guarantors, the Trustee, and Wilmington Savings Fund Society, FSB, as Collateral Trustee, have heretofore executed and
delivered an indenture, dated as of June 6, 2014 (as amended, restated, supplemented or otherwise modified by this First Supplemental Indenture, the “Indenture”), providing for the issuance by the Company of 10.0% Convertible
Senior Secured Notes due 2017; 
 WHEREAS, Section 14.02 of the Indenture provides, among other things, that the Company, the
Guarantors and the Trustee may, with the consent of Requisite Holders, enter into an indenture or indentures supplemental thereto for the purpose of adding any provisions to or changing in any manner or eliminating any of the provisions of the
Indenture or of modifying in any manner the rights of the Holders under the Indenture; 
 WHEREAS, the Company has requested that the
Requisite Holder consent to the issuance of the 2014 Warrants, the incurrence of Indebtedness by Company under the 2014 Warrants and the Company’s entry into this First Supplemental Indenture, and the Requisite Holder desires to consent to the
issuance of the 2014 Warrants, the incurrence of Indebtedness by Company under the 2014 Warrants and the Company’s entry into this First Supplemental Indenture; and 

WHEREAS, the Company has requested that the Trustee enter into this First Supplement Indenture, and the Trustee has agreed to enter into this
First Supplemental Indenture on the terms set forth below. 
 NOW, THEREFORE, in consideration of the foregoing and for other good and
valuable consideration, the receipt of which is hereby acknowledged, the Company, the Guarantors, the Trustee and the Requisite Holder hereby covenant and agree as follows: 

AGREEMENT 
 1. Consent
to Issuance of the 2014 Warrants. Notwithstanding any term or provision in the Indenture or any other Indenture Document to the contrary, the Requisite Holder hereby consents, effective as of the date hereof, to the offering and issuance of the
2014 Warrants, the execution and delivery of the 2014 Warrant Agreement (as defined below), and the incurrence of the Indebtedness under the 2014 Warrants provided that (a) the initial issuance of the 2014 Warrants shall have been consummated
on or before August 15, 2014, (b) such 2014 Warrants are on terms and conditions consistent in all material respects with the terms and conditions specified on Annex A attached hereto or as modified so long as such modifications are
not adverse in any respect to the Trustee and the Holders, 

 
and (c) the consent set forth herein shall not constitute an approval of a transaction under Section 9.01(m) of the Indenture which would enable the Company to make a cash payments on
account of the 2013 Warrants and/or the 2014 Warrants (without triggering an Event of Default). 
 2. Effectiveness; Amendments to
Indenture. This First Supplemental Indenture shall become effective immediately upon its execution and delivery by each of the Company, the Guarantors, the Trustee and the Requisite Holder; provided that the amendments to the Indenture
contemplated in this First Supplemental Indenture shall only become operative upon the date on which the first 2014 Warrant is issued (the “First Issuance Date”) and so long as the conditions specified in Section 1 of this
First Supplemental Indenture have been satisfied. The Company shall notify the Trustee (i) of the issuance of such first 2014 Warrant promptly following the First Issuance Date and shall specify the date of such issuance or (ii) promptly
after the Company shall determine that such issuance will not occur. 
 (a) Section 1.01 of the Indenture is hereby amended by adding
the following definitions in the appropriate alphabetical order: 
 “2014 Warrant Agreement” means the
Common Stock Unit Warrant Agreement, dated on or about August 5, 2014, by and between the Company and American Stock Transfer & Trust Company, LLC, acting as warrant agent, as amended, modified, supplemented or restated from time to
time. 
 “2014 Warrants” means the warrants issued by the Company from time to time pursuant to the 2014
Warrant Agreement and all other documents, instruments and agreements evidencing or governing such warrants or providing for any other right in respect thereof, each as amended, modified, supplemented or restated from time to time in accordance with
the 2014 Warrant Agreement. 
 “2014 Warrant Issuance Date” means the first date on which a 2014 Warrant is
issued. 
 (b) The definition of “Disqualified Equity Interests” contained in Section 1.01 of the Indenture is
hereby amended by amending and restating the last sentence appearing in such definition as follows: 
 “The foregoing to the contrary
notwithstanding, “Disqualified Equity Interests” shall not include the 2013 Warrants or 2014 Warrants solely as a result of the Black Scholes Value payments required in connection therewith.” 

(c) Section 4.30(s) of the Indenture is hereby amended by amending and restating such section in its entirety as follows: 

“(s) Indebtedness in respect of the 2013 Warrants and the 2014 Warrants.” 

(d) Section 4.33 of the Indenture is hereby amended by amending and restating clauses (vii) and (xii) in their entirety
as follows: 
 “(vii) Restricted Payments required in connection with the exercise of warrants or the conversion of convertible
Indebtedness are permitted to the extent that such conversion is for Equity Interests of the Company (and does not involve any cash payments other than in regards to cash payments made in lieu of issuing fractional shares or payment obligations
required under the terms of the 2013 Warrants or 2014 Warrants);” 

 “(xii) cash payments payable on account of the 2013 Warrants in effect on the date hereof,
the 2014 Warrants in effect as of the 2014 Warrant Issuance Date, and the cashless exercise of options and warrants in accordance with their terms;” 

(e) Section 9.01(m) of the Indenture is hereby amended by amending and restating the section in its entirety as follows: 

“(m) the earlier to occur of (i) the occurrence of any event, circumstance or transaction that would entitle the holders of the 2013
Warrants or 2014 Warrants to any cash payment from the Company (or otherwise require the Company to make an offer make a cash payment to such holders) under the 2013 Warrants or 2014 Warrants other than in lieu of the issuance of fractional shares
or (ii) the making of a cash payment (or any offer to make such payment) under the 2013 Warrants or 2014 Warrants (in each case, other than in lieu of the issuance of fractional shares ) provided that in each case, no Event of Default will be
triggered if the Requisite Holders approve the transaction that triggers the obligation to make a cash payment on account of the 2013 Warrants or the 2014 Warrants.” 

3. Indenture Supplemented; Ratification of Indenture. This First Supplemental Indenture is supplemental to the Indenture and does and
shall be deemed to form a part of, and shall be construed in connection with and as part of, the Indenture for any and all purposes. Except as specifically modified herein, the Indenture, as amended, restated, supplemented or otherwise modified by
this First Supplemental Indenture, and the Notes, are in all respects ratified and confirmed, and shall remain in full force and effect in accordance with their terms. 

4. Trustee. Except as otherwise expressly provided herein, no duties, responsibilities or liabilities are assumed, or shall be
construed to be assumed, by the Trustee by reason of this First Supplemental Indenture. This First Supplemental Indenture is executed and accepted by the Trustee subject to all the terms and conditions set forth in the Indenture with the same force
and effect as if those terms and conditions were repeated at length herein and made applicable to the Trustee with respect hereto. 
 5.
Governing Law. THIS FIRST SUPPLEMENTAL INDENTURE SHALL BE GOVERNED BY, AND CONSTRUED IN ACCORDANCE WITH, THE LAWS OF THE STATE OF NEW YORK (OR, TO THE EXTENT REQUIRED, THE LAW OF THE JURISDICTION IN WHICH THE COLLATERAL IS LOCATED), WITHOUT
REGARD TO CONFLICTS OF LAWS PRINCIPLES THEREOF. 
 6. Multiple Originals. The parties may sign any number of copies of this First
Supplemental Indenture. Each signed copy shall be an original, but all of them together represent the same agreement. One signed copy is enough to prove this First Supplemental Indenture. Delivery of an executed counterpart by facsimile or PDF shall
be as effective as delivery of a manually executed counterpart thereof. 
 7. Waiver of Jury Trial. EACH OF THE PARTIES HERETO HEREBY
IRREVOCABLY WAIVES, TO THE FULLEST EXTENT PERMITTED BY APPLICABLE LAW, ANY AND ALL RIGHT TO TRIAL BY JURY IN ANY LEGAL PROCEEDING ARISING OUT OF OR RELATING TO THIS FIRST SUPPLEMENTAL INDENTURE, THE NOTES OR THE TRANSACTION CONTEMPLATED THEREBY.

 8. Consent to Jurisdiction. Each of the Parties hereto hereby irrevocably and
unconditionally submits, for itself and its property, to the nonexclusive jurisdiction of any competent New York State court or federal court of the United States sitting in the State and City of New York, County of New York and Borough of
Manhattan, and any appellate court from any thereof, in any action or proceeding arising out of or relating to this First Supplemental Indenture or the Notes, or for recognition or enforcement of any judgment, and each of the parties hereto hereby
irrevocably and unconditionally agrees that all claims in respect of any such action or proceeding may be heard and determined in such state court sitting in the State and City of New York, County of New York and Borough of Manhattan or, to the
extent permitted by law, in such federal court sitting in the State and City of New York, County of New York and Borough of Manhattan. 
 Each of the
Parties hereto hereby irrevocably and unconditionally waives, to the fullest extent it may legally and effectively do so, any objection which it may now or hereafter have to the laying of venue of any suit, action proceeding arising out of or
relating to this First Supplemental Indenture or the Notes in any such New York State or federal court. Each of the parties hereto hereby irrevocably waives, to the fullest extent permitted by law, the defense of an inconvenient forum to the
maintenance of such action or proceeding in any such court. 
 [Remainder of the page intentionally left blank] 

 
			
	COMPANY:
	
	GEVO, INC.
		
	By:	 	 /s/ Mike Willis

	Name:	 	Mike Willis
	Title:	 	Chief Financial Officer
	
	GUARANTORS:
	
	AGRI-ENERGY, LLC
		
	By:	 	 /s/ Mike Willis

	Name:	 	Mike Willis
	Title:	 	Chief Financial Officer
	
	GEVO DEVELOPMENT, LLC
		
	By:	 	 /s/ Mike Willis

	Name:	 	Mike Willis
	Title:	 	Chief Financial Officer
	
	TRUSTEE:
	
	 WILMINGTON SAVINGS FUND SOCIETY, FSB,

as Trustee

		
	By:	 	 /s/ Kristin L. Moore

	Name:	 	Kristin L. Moore
	Title:	 	Vice President
	
	REQUISITE HOLDERS:
	
	WB GEVO, LTD.
		
	By:	 	 /s/ Michael McCormick

	Name:	 	Michael McCormick
	Title:	 	DirectorEX-10.1

 Exhibit 10.1 

CONSENT AND SECOND AMENDMENT TO TERM LOAN AGREEMENT 

CONSENT AND SECOND AMENDMENT TO TERM LOAN AGREEMENT (this “Amendment”), dated July 31, 2014,
by and among Gevo, Inc. a Delaware corporation (the “Borrower”), the Guarantors party hereto (the “Guarantors” and together with the Borrower, each a
“Credit Party” and collectively, the “Credit Parties”), the Lenders (as defined below), and WB Gevo, Ltd. (as successor in interest to Whitebox Advisors LLC), as
administrative agent (in such capacity, the “Administrative Agent”). 
 WHEREAS, the Credit
Parties, the Administrative Agent and the lenders party thereto from time to time (“Lenders”) entered into that certain Term Loan Agreement dated as of May 9, 2014 (as amended by that certain First Amendment to Term Loan
Agreement and Pledge and Security Agreement dated as of June 6, 2014, and as may be further amended, amended and restated, modified, supplemented, extended, renewed, restated or replaced from time to time, the “Term Loan
Agreement”); 
 WHEREAS, the Borrower has requested that the Administrative Agent and Lenders consent to the issuance of the
2014 Warrants and amend the Term Loan Agreement to provide for the issuance of the 2014 Warrants; 
 WHEREAS, the Lenders and the Credit
Parties desire to amend the Term Loan Agreement subject to the terms and conditions set forth herein. 
 NOW, THEREFORE, in consideration of
the mutual promises contained herein, and for other good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, the parties hereto hereby agree as follows: 

1. Defined Terms. Unless otherwise defined herein, all capitalized terms used herein (including the recitals hereto) shall have the
respective meaning assigned to such terms in the Term Loan Agreement as amended by this Amendment. 
 2. Consent to Issuance of the 2014
Warrants. Notwithstanding any term or provision in the Term Loan Agreement or any other Loan Document to the contrary, Administrative Lender and Lenders consent, effective upon the date hereof, to the offering and issuance of the 2014
Warrants, the execution and delivery of the 2014 Warrant Agreement (as defined below), and the incurrence of the Indebtedness under the 2014 Warrants provided that (a) the initial issuance of the 2014 Warrants shall have been
consummated on or before August 15, 2014, (b) such 2014 Warrants are on terms and conditions consistent in all material respects with the terms and conditions specified on Annex A attached hereto or as modified so long as such
modifications are not adverse in any respect to Administrative Agent and Lenders, (c) the consent set forth herein shall not constitute an approval of a transaction under Section 7.1(q) of the Term Loan Agreement which would enable the
Borrower to make cash payment(s) on account of the 2013 Warrants and/or the 2014 Warrants (without triggering an Event of Default), and (d) the issuance of the 2014 Warrants and/or the exercise thereof does not constitute a Change in Control.

 3. Amendments to the Term Loan Agreement. 

(a) Appendix I of the Term Loan Agreement is hereby amended by adding the following definitions in the appropriate alphabetical order:

 “2014 Warrant Agreement” means the Common Stock Unit Warrant Agreement, dated on or about August 5,
2014, by and between the Borrower and American Stock Transfer & Trust Company, LLC, acting as warrant agent, as amended, modified, supplemented or restated from time to time. 

“2014 Warrants” means the warrants issued by the Borrower from time to time pursuant to the 2014 Warrant
Agreement and all other documents, instruments and agreements evidencing or governing such warrants or providing for any other right in respect thereof, each as amended, modified, supplemented or restated from time to time in accordance with the
2014 Warrant Agreement. 
 “2014 Warrant Issuance Date” means the first date on which a 2014 Warrant is
issued. 
 (b) The definition of “Disqualified Equity Interests” set forth on Appendix I of the Term Loan Agreement
is hereby amended by amending and restating the last sentence appearing in such definition as follows: 
 “The foregoing to the contrary
notwithstanding, “Disqualified Equity Interests” shall not include the 2013 Warrants or 2014 Warrants solely as a result of the Black Scholes Value payments required in connection therewith.” 

(c) Section 6.2(s) of the Term Loan Agreement is hereby amended by amending and restating such section in its entirety as follows:

 “(s) Debt in respect of the 2013 Warrants and the 2014 Warrants.” 

(d) Section 6.5 of the Term Loan Agreement is hereby amended by amending and restating clauses (vii) and (xii) in their
entirety as follows: 
 “(vii) Restricted Payments required in connection with the exercise of warrants or the conversion of convertible
Debt are permitted to the extent that such conversion is for Equity Interests of the Borrower (and does not involve any cash payments other than in regards to cash payments made in lieu of issuing fractional shares or payment obligations required
under the terms of the 2013 Warrants or 2014 Warrants);” 
 “(xii) cash payments payable on account of the 2013 Warrants in effect
on the date hereof, the 2014 Warrants in effect as of the 2014 Warrant Issuance Date, and the cashless exercise of options and warrants in accordance with their respective terms;” 

  
 2 

 (e) Section 7.1(q) of the Term Loan Agreement is hereby amended by amending and
restating the section in its entirety as follows: 
 “2013 Warrants and 2014 Warrants. The earlier to occur of (i) the
occurrence of any event, circumstance or transaction that would entitle the holders of the 2013 Warrants or 2014 Warrants to any cash payment from the Borrower (or otherwise require the Borrower to make an offer to make a cash payment to such
holders) under the 2013 Warrants or 2014 Warrants other than in lieu of the issuance of fractional shares or (ii) the making of a cash payment (or any offer to make such payment) under the 2013 Warrants or 2014 Warrants (in each case, other
than in lieu of the issuance of fractional shares) provided that in each case, no Event of Default will be triggered if the Requisite Lenders approve the transaction that triggers the obligation to make a cash payment on account of the 2013 Warrants
or the 2014 Warrants;” 
 4. Effect of this Amendment. Except as expressly amended, consented to or waived hereby, the Term Loan
Agreement and the other Loan Documents are ratified and confirmed in all respects and shall remain in full force and effect in accordance with their respective terms. Except as expressly set forth herein, the terms of this Amendment shall not be
deemed (i) a waiver of any Default or Event of Default, (ii) a consent, waiver or modification with respect to any term, condition, or obligation of the Borrower or any other Credit Party in the Term Loan Agreement or any other Loan
Document, (iii) a consent, waiver or modification with respect to any other event, condition (whether now existing or hereafter occurring) or provision of the Loan Documents or (iv) to prejudice any right or remedy which the Administrative
Agent or any Lender may now or in the future have under or in connection with the Term Loan Agreement or any other Loan Document. The parties’ agreement to enter into this Amendment shall not obligate or commit the Administrative Agent or
Lender(s) to provide any other consents or waivers under the Term Loan Agreement or the other Loan Documents in the future, whether for purposes similar to those described herein or otherwise. 

5. Conditions Precedent To Effectiveness of this Amendment. This Amendment shall become effective upon the execution of this Amendment
by the Lenders and Credit Parties and the execution and delivery of that certain First Supplemental Indenture dated as of the date hereof by and among the Borrower, the Guarantors (as defined therein), the Requisite Holder (as defined therein) and
Wilmington Savings Fund Society, FSB as Trustee. 
 6. Miscellaneous. 

(a) Notices. All notices required to be made under this Amendment shall be made in the manner and at the address set forth in
Section 10.2 of the Term Loan Agreement. 
 (b) Reference to Term Loan Agreement. From and after the effectiveness of this
Amendment, all references in the herein and the other Loan Documents to the Term Loan Agreement shall mean the Term Loan Agreement as amended hereby and as hereafter modified, amended, restated or supplemented from time to time. 

(c) Entire Agreement. This Amendment shall be deemed to be a Loan Document and, together with the other Loan Documents and the
agreements, documents and instruments contemplated hereby, constitutes the entire understanding of the parties with respect to the subject matter hereof and thereof, and any other prior or contemporaneous agreements, whether written or oral, with
respect hereto or thereto are expressly superseded hereby and thereby. 

  
 3 

 (d) Counterparts. This Amendment may be executed in any number of counterparts and by
different parties on separate counterparts, each of which, when executed and delivered, shall be deemed to be an original, and all of which, when taken together, shall constitute but one and the same Amendment. Delivery of an executed counterpart of
this Amendment by facsimile or .pdf shall be equally as effective as delivery of an original executed counterpart of this Amendment. Any party delivering an executed counterpart of this Amendment by facsimile or .pdf also shall deliver an original
executed counterpart of this Amendment but the failure to deliver an original executed counterpart shall not affect the validity, enforceability, and binding effect of this Amendment. 

(e) Governing Law; Venue; Jury Trial. THIS AMENDMENT AND THE RIGHTS AND OBLIGATIONS OF THE PARTIES HEREUNDER SHALL BE GOVERNED BY, AND
CONSTRUED IN ACCORDANCE WITH, THE CHOICE OF LAW AND VENUE PROVISIONS SET FORTH IN SECTION 10.12 OF THE TERM LOAN AGREEMENT, AND SHALL BE SUBJECT TO THE JURY TRIAL WAIVER SET FORTH IN SECTION 10.14 OF THE TERM LOAN AGREEMENT. 

(f) Guarantors. Each Guarantor, for value received, hereby expressly consents and agrees to the Borrower’s execution and delivery
of this Amendment, and to the performance by the Borrower of its agreements and obligations hereunder. This Amendment and the performance or consummation of any transaction or matter contemplated under this Amendment, shall not limit, restrict,
extinguish or otherwise impair any Guarantor’s liability to the Administrative Agent and/or Lenders with respect to the payment and other performance obligations of such Guarantor pursuant to the Guarantees. Each Guarantor hereby ratifies,
confirms and approves its Guarantee and acknowledges that it is unconditionally liable to the Administrative Agent and Lenders for the full and timely payment of the Guaranteed Obligations (on a joint and several basis with the other Guarantors).
Each Guarantor hereby acknowledges that it has no defenses, counterclaims or set-offs with respect to the full and timely payment of any or all Guaranteed Obligations. 

[Remainder of Page Intentionally Left Blank; Signature Pages to Follow] 

  
 4 

 IN WITNESS WHEREOF, each of the parties hereto has duly executed this Consent and Second
Amendment to Term Loan Agreement as of the date first written above. 
  

			
	BORROWER:
	
	 GEVO, INC.,
 a Delaware
corporation

		
	By:	 	 /s/ Mike Willis

	Name:	 	Mike Willis
	Title:	 	Chief Financial Officer
	
	GUARANTORS:
	
	AGRI-ENERGY, LLC, a Minnesota limited liability company
		
	By:	 	 /s/ Mike Willis

	Name:	 	Mike Willis
	Title:	 	Chief Financial Officer
	
	GEVO DEVELOPMENT, LLC, a Delaware limited liability company
		
	By:	 	 /s/ Mike Willis

	Name:	 	Mike Willis
	Title:	 	Chief Financial Officer

 [Signature Page to Consent and Second Amendment to Term Loan Agreement] 

			
	ADMINISTRATIVE AGENT:
	
	WB GEVO, LTD.
		
	By:	 	 /s/ Michael McCormick

	Name:	 	Michael McCormick
	Title:	 	Director

 [Signature Page to Consent and Second Amendment to Term Loan Agreement] 

			
	LENDER:
	
	WB GEVO, LTD.
		
	By:	 	 /s/ Michael McCormick

	Name:	 	Michael McCormick
	Title:	 	Director

 [Signature Page to Consent and Second Amendment to Term Loan Agreement]

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