EX-4.1



 Exhibit 4.1 

MHR Fund Management LLC 

1345 Avenue of the Americas, 42nd Floor 

New York, NY 10105 
 Telephone:
(212) 262-0005 
 Facsimile: (212) 262-9356 

November 10, 2015 
 Emisphere Technologies, Inc. 

4 Becker Farm Road, Suite 103 
 Roseland, NJ 07068, USA 

Attention: President and Chief Executive Officer 
 Ladies and
Gentlemen: 
 Reference is made to (a) the Second Amended and Restated 13% Senior Secured Convertible Notes (the “Convertible
Notes”), dated as of August 20, 2014, by Emisphere Technologies, Inc. (the “Company”) in favor of each of (i) MHR Institutional Partners IIA LP, (ii) MHR Capital Partners Master Account LP, (iii) MHR
Capital Partners (100) LP and (iv) MHR Institutional Partners II LP (each, a “MHR Entity” and, collectively, the “MHR Entities”) and (b) the Senior Secured Loan Agreement (the “Loan
Agreement”), dated as of August 20, 2014, by and among the Company and the MHR Entities, as may be amended, restated or otherwise modified from time to time. 

WHEREAS, under the Loan Agreement and the Convertible Notes, the Company is required to have Net Sales (as such term is defined in the Loan
Agreement and in the Convertible Notes) of Eligen-B12 during the Fiscal Year (as such term is defined in the Loan Agreement and in the Convertible Notes) ended December 31, 2015 of at least $4.3 million (the “2015 Net Sales
Milestone”); 
 WHEREAS, the failure to achieve the 2015 Net Sales Milestone would result in the occurrence of an Event of Default
(as such term is defined in the Loan Agreement and in the Convertible Notes) under the Loan Agreement and the Convertible Notes; and 

WHEREAS, the Company has advised the MHR Entities that it does not expect to meet the 2015 Net Sales Milestone and has requested that the MHR
Entities waive any Event of Default that will arise under the Loan Agreement and Convertible Notes as a result of the Company’s failure to meet the 2015 Net Sales Milestone. 

NOW, THEREFORE, the MHR Entities agree as follows: 

1. This letter shall constitute a waiver of (i) any Event of Default (as such term is defined in the Loan Agreement) under
Section 8(a)(xiii) of the Loan Agreement and (ii) any Event of Default (as such term is defined in the Convertible Notes) under Section 8(a)(xiii) of the Convertible Notes that, in either case, may arise directly as a result of the
Company’s failure to meet the 2015 Net Sales Milestone. 

  
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 2. Except as expressly set forth herein, the Loan Agreement and Convertible Notes are unmodified
and remain in full force and effect. Execution of this waiver by the MHR Entities does not and shall not constitute a waiver of or otherwise affect any rights or remedies to which the MHR Entities are or may at any time be entitled pursuant to the
Loan Agreement or Convertible Notes nor, except as expressly set forth herein, shall the same constitute at any time a waiver of any default or event of default with respect to the Loan Agreement or the Convertible Notes. Except as expressly set
forth herein, this letter shall not be used in connection with or affect any other requests by the Company to the MHR Entities under either the Loan Agreement or the Convertible Notes. 

[Remainder of Page Intentionally Left Blank] 

  
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	Very truly yours,
	
	MHR Institutional Partners II LP
		
	By:	 	MHR Institutional Advisors II LLC,
		 	its General Partner
			
		 	By:	 	 /s/ Janet Yeung

		 	Name:	 	Janet Yeung
		 	Title:	 	Authorized Signatory
	
	MHR Institutional Partners IIA LP
		
	By:	 	MHR Institutional Advisors II LLC,
		 	its General Partner
			
		 	By:	 	 /s/ Janet Yeung

		 	Name:	 	Janet Yeung
		 	Title:	 	Authorized Signatory
	
	MHR Capital Partners Master Account LP
		
	By:	 	MHR Advisors LLC,
		 	its General Partner
			
		 	By:	 	 /s/ Janet Yeung

		 	Name:	 	Janet Yeung
		 	Title:	 	Authorized Signatory
	
	MHR Capital Partners (100) LP
		
	By:	 	MHR Advisors LLC,
		 	its General Partner
			
		 	By:	 	 /s/ Janet Yeung

		 	Name:	 	Janet Yeung
		 	Title:	 	Authorized Signatory

 [MHR Eligen-B12 Waiver]