Document:

Exhibit10.13BKarsnerConsultingAgreement01-01-2014

Exhibit 10.13B
CODEXIS, INC.

CONSULTING AGREEMENT

THIS AGREEMENT is made by CODEXIS, INC., a Delaware corporation (“Codexis”), and Alexander A. Karsner (“Consultant”) effective as of the 1st day of January, 2014 (the “Effective Date”), for the purpose of setting forth the exclusive terms and conditions by which Codexis will acquire Consultant’s services on a temporary basis.  In consideration of the mutual obligations specified in this Agreement, and any compensation paid to Consultant for Consultant’s services, the parties agree to the following:

1.Consulting Services.  Consultant is hereby retained by Codexis to provide Codexis with strategic advisory services, as requested by Codexis from time to time. Consultant shall perform to the best of Consultant’s ability such services at such places and such times as mutually agreed to by Codexis and Consultant. 
2.    Conflicts of Interest.  Consultant represents that Consultant is not currently engaged in any agreement or arrangement with any third party that might reasonably conflict with the terms of this Agreement.  If Consultant becomes so engaged during the term of this Agreement, Consultant will notify Codexis in writing within ten (10) days of entering into such agreement, and will use Consultant’s best efforts and cooperate with Codexis to avoid and/or minimize the adverse consequences of any potential conflict.
3.    Compensation.  As the only consideration due to Consultant for Consultant’s services under this Agreement, Codexis shall provide Consultant the compensation set forth in this Section 3 as follows:
(a)    Codexis shall pay Consultant at a rate of $30,000 per quarter for all work performed for Codexis by Consultant as a consultant to Codexis in accordance with this Agreement.  In addition, Codexis shall reimburse Consultant for reasonable expenses incurred by Consultant in connection with the work performed for Codexis by Consultant, including all reasonable costs and expenses incurred by Consultant in connection with such work for travel, transportation, lodging, and meals, provided that such costs and expenses are in accordance with Codexis policies and that Consultant provides Codexis with all receipts and other documentation related to such costs and expenses.  Consultant shall invoice Codexis quarterly (attn: Accounts Payable) for Consultant’s services performed under this Agreement.  Codexis shall pay all undisputed invoices within thirty (30) days from receipt thereof.  
(b)    The vesting schedule for the shares of restricted stock (the “Restricted Stock”) granted to Consultant on January 24, 2013 shall be amended such that such number of shares of Restricted Stock originally scheduled to vest on January 24, 2015 shall vest on the Expiration Date as follows, such that the maximum of 7,184 shares would vest if the Expiration Date is June 30, 2014: 
 
    Number of shares to vest on Expiration Date = 7,184 * (N/181) 
    Where N = the number of calendar days elapsed in 2014 as of the Expiration Date,     

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inclusive of the Expiration Date 
 
The vesting schedule for all other shares of Restricted Stock will remain unchanged, which vesting shall be contingent upon continued service to Codexis though the applicable vesting date in accordance with the terms of the agreement evidencing the Restricted Stock award.  Any shares of Restricted Stock that are unvested on the date Consultant ceases to provide services to Codexis shall be automatically forfeited.
(c)    For the avoidance of doubt, the compensation provided by this Section 3 shall be in addition to any compensation Consultant otherwise becomes entitled to as a member of the board of directors of Codexis (the “Board”). 
4.    Protection of Confidential Information.   
(a)    In the course of the Consultant’s performance hereunder, Consultant may receive and otherwise be exposed to confidential and proprietary information relating to Codexis business practices, strategies and technologies, as well as information belonging to third parties as to which Codexis has an obligation of confidentiality (collectively, “Confidential Information”).  Confidential Information is broadly defined and includes, without limitation, all oral and written information that: (i) has or could have commercial value or other utility in the businesses in which Codexis is engaged or in which it contemplates engaging, (ii) is supplied to Consultant by Codexis with the legend “Confidential Information” or other designation of confidentiality, (iii) Codexis is under an obligation of confidentiality with any third party, and/or (iv) if disclosed without authorization, could be detrimental to the interests of Codexis or its third party business partners, whether or not this information is identified as Confidential Information.  By example, and without limitation, Confidential Information includes scientific and technical information like Codexis’ research programs, product development, biological materials, research methods, related products, technology, inventions, patent applications and trade secrets, and information concerning Codexis’ business affairs and operations including fields of interests, concepts, techniques, processes, designs, cost data,  financial and marketing information, personnel and customer lists, and any other similar information.  Confidential Information does not include information that as demonstrated by written evidence: (i) was generally and publicly known in the relevant trade or industry; (ii) was known to, and freely usable by, Consultant before Consultant’s engagement by Codexis; (iii) was rightfully received by Consultant from a third party after the time it was disclosed or obtained hereunder, provided that such third party was not under an obligation of confidence with Codexis at the time of the third party’s disclosure to Consultant; or (iv) is independently developed by Consultant without use of or reference to the Confidential Information and without breach of this Agreement. 
(b)    At all times during and after Consultant’s service to Codexis, Consultant shall hold in trust, keep strictly confidential and not disclose to any third party, or make any use of, the Confidential Information, except as may be necessary in the course of Consultant’s service to Codexis, without the prior written consent of Codexis.  Consultant agrees to abide by all policies established by Codexis for the protection of Confidential Information, and to take reasonable and necessary security precautions to safeguard Confidential Information, including, without limitation, the protection of documents from theft, unauthorized duplication and discovery of contents, and restrictions on access by other persons.  Consultant further agrees not 

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to cause the transmission, removal, or transport of any Confidential Information from Codexis’ principal place of business, or any other place of business as specified by Codexis without the prior written approval of Codexis, except as required in the course of Consultant’s service to Codexis.
(c)    Consultant acknowledges that unauthorized use or disclosure of Confidential Information may be highly prejudicial to the interests of Codexis or its third party business partners, an invasion of privacy, or a misappropriation or improper disclosure of trade secrets.
(d)    Consultant acknowledges that Codexis has received and in the future may receive Confidential Information from third parties subject to a duty on Codexis’ part to maintain the confidentiality of the information and to use it only for certain limited purposes.  Consultant agrees to hold all such Confidential Information in the strictest confidence and in compliance with the terms of any agreement Codexis may have with such third parties, and not to disclose such Confidential Information to any person, firm or corporation or to use it except as necessary in carrying out Consultant’s duties for Codexis, consistent with the terms of any agreement Codexis may have with such third parties. 
(e)    Consultant acknowledges that any unauthorized use or disclosure to third parties of Confidential Information during Consultant’s service to Codexis may lead to immediate termination, and any unauthorized use or disclosure during or after Consultant’s service to Codexis can lead to legal action by Codexis and/or a third party.
5.    Consultant’s Obligations on Termination of Service.
(a)    Return of Codexis Property.  Upon separation from service with Codexis for any reason, Consultant will promptly deliver to Codexis all documents in Consultant’s possession or control pertaining to (i) Consultant’s service to Codexis and (ii) the Confidential Information of Codexis or of its third party business partners, except that Consultant may retain personal copies of any documents created by Consultant and provided to Codexis, records relating to Consultant’s compensation and this Agreement.  Consultant also agrees to return to Codexis all equipment, files, software programs and other personal property belonging to Codexis on separation from service with Codexis.  Consultant will not retain any written or other tangible materials (in hard copy or electronic form) that evidence, contain or reflect Confidential Information of Codexis or of a third party that was provided to Codexis.
(b)    Protection of Codexis’ Confidential Information.  Consultant will protect the value of Codexis’ Confidential Information and will prevent their theft or unlawful disclosure, including, without limitation, following Consultant’s separation from service with Codexis.  Consultant will not use or disclose Confidential Information for Consultant’s benefit (or for the benefit of any third party) or to the detriment of Codexis or any of its Third Party Business Partners.
(c)    Non-Interference with Codexis Employees.  Consultant agrees that, both during Consultant’s service to Codexis and for a period of twenty four (24) months, or to the maximum extent permitted by law if shorter, following separation from service with Codexis for any reason, Consultant will not disrupt, damage, impair or interfere with Codexis’ business by 

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recruiting, soliciting or otherwise inducing any Codexis employee or exclusive consultant to leave the employ or service of Codexis, which means that Consultant will not (i) disclose to any third party the names, backgrounds or qualifications of any employees or exclusive consultants or otherwise identify them as potential candidates for employment or other service; or (ii) personally or through any other person approach, recruit, interview or otherwise solicit employees or exclusive consultants to work for Consultant or any other employer or service recipient.
(d)    Non-Solicitation of Customers Using Confidential Information.  Consultant also agrees that, both during service to Codexis and thereafter, Consultant will not call on, solicit, or take away (directly or indirectly), on behalf of Consultant or any third party, the business of any client or customer of Codexis, whether past, present or prospective, using any Confidential Information.
6.    Ownership of Work Product.  Consultant shall promptly disclose in writing to Codexis complete information concerning all know-how, inventions conceived or reduced to practice by Consultant, and all copyrightable material written by Consultant, which know-how, inventions or copyrightable materials are created, generated or developed by Consultant in the course of Consultant’s performance of Consultant’s services hereunder that are derived from any Confidential Information of Codexis (collectively, “Work Product”).  Consultant agrees that all such Work Product is the sole property of Codexis and hereby assigns to Codexis, its successors and assigns, all right, title and interest in the same.  Consultant represents and warrants to Codexis that the Work Product is and shall remain free and clear of all liens, claims, encumbrances or demands of third parties, including any claims by any such third parties of any right, title or interest in or to the Work Product arising out of any trade secret, copyright or patent, and that Consultant is not bound by any agreement or court order that would conflict with the terms of this Agreement
7.    Injunctive Relief.  Consultant acknowledges that it would be difficult for Codexis to measure actual damages resulting from any breach by Consultant of Sections 4 through 6 of this Agreement, and that money damages alone would be an inadequate remedy for any such breach.  Accordingly, Consultant agrees that if Consultant breaches any provision of Sections 4 through 6, Codexis will be entitled, in addition to any other remedies it may have, to specific performance, injunctions, or other appropriate orders to correct or restrain any such breach by Consultant, without showing or proving any actual damage sustained by Codexis or posting any bond or other security.
8.    Attorney Fees.  If any action is necessary to enforce this Agreement, including any action under Paragraph 7, the prevailing party will be entitled to recover its reasonable costs and attorney fees.
9.    Indemnification and Release.  Consultant agrees to take all necessary precautions to prevent injury to any persons (including employees of Codexis or damage to property (including Codexis property), and shall indemnify, defend, save, protect and hold Codexis and its officers, agents, directors, employees and customers harmless against all claims, losses, expenses (including reasonable attorneys’ and expert witnesses’ fees and costs) and injuries to person or property (including death) (collectively, “Claims”) resulting in any way 

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from any gross negligence or willful misconduct of Consultant, or resulting from any breach by Consultant of Consultant’s obligations, representations or warranties under this Agreement.  Codexis agrees to indemnify, defend, save, protect and hold Consultant harmless against all Claims resulting in any way from any gross negligence or willful misconduct of Codexis, or resulting from any breach by Codexis of its obligations, representations or warranties under this Agreement, except to the extent the same are the responsibility of Consultant under the preceding sentence.  
10.    Term and Termination.  Unless previously terminated as provided herein, this Agreement shall expire on June 30, 2014.  The “Expiration Date” shall mean the earlier to occur of (i) the early termination of this Agreement in accordance with this Section 10 or (ii) June 30, 2014.  Either Codexis or Consultant may terminate this Agreement at any time for any reason, effective upon written notice to the other party.  Termination of this Agreement by Codexis shall require approval by the Board.  In connection with any termination of this Agreement, Consultant shall cease work unless otherwise advised by Codexis, Consultant shall notify Codexis of costs and expenses incurred up to the Expiration Date and Codexis will pay Consultant fees for services performed through the Expiration Date.  In connection with expiration or any termination of this Agreement, Consultant shall return to Codexis all copies of all Confidential Information and Work Product under this Agreement.  Sections 4, 5, 6, 7, 8, 9, 10, 11, 12, and 13 hereof shall survive expiration or any termination of this Agreement.
11.    Compliance with Applicable Laws.  Consultant represents and warrants to Codexis that all work performed under this Agreement and all Work Product will comply with all applicable laws and regulations.  
12.    Independent Contractor.  Consultant is an independent contractor, is not an agent or employee of Codexis and is not authorized to act on behalf of Codexis. Consultant will not be eligible for any employee benefits, nor will Codexis make deductions from any amounts payable to Consultant for taxes.  Taxes for any amounts paid to Consultant hereunder shall be the sole responsibility of Consultant.  Prior to any Codexis payments to Consultant, Consultant agrees to submit a completed W-9 form and tax identification number to Codexis (attn:  Accounts Payable).
13.    General.  Consultant may not assign this Agreement or delegate any of Consultant’s duties under this Agreement without Codexis prior written consent.  This Agreement constitutes the parties’ final, exclusive and complete understanding and agreement with respect to the subject matter hereof, and supersedes all prior and contemporaneous understandings and agreements regarding the subject matter hereof.  This Agreement may not be waived, modified or amended unless mutually agreed upon in writing by both parties.  In the event any provision of this Agreement is found to be legally unenforceable, such unenforceability shall not prevent enforcement of any other provision of the Agreement.  This Agreement shall be governed by the laws of the State of California, without regard to its conflicts of laws principles.  Any notices required or permitted hereunder shall be given to the appropriate party at the address specified below or at such other address as the party shall specify in writing.  Such notice shall be deemed given upon personal delivery or telecopy (with machine confirmation of receipt), or three (3) days after the date of mailing if sent by certified or registered mail, postage prepaid.

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(Signature page follows)

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IN WITNESS WHEREOF, the parties hereto have executed this Agreement as of the Effective Date first set forth above.

CODEXIS, INC.            CONSULTANT

By:/s/Doug T. Sheehy            /s/Alexander A. Karsner            
Name: Doug Sheehy                    Alexander A. Karsner
Title: Senior Vice President, General Counsel 
           and Secretary    

CODEXIS ADDRESS:                CONSULTANT ADDRESS:
                
200 Penobscot Drive                    7009 Deep Creek Court
Redwood City, CA 94063                Bethesda, MD  20817
Attention:  General Counsel        
Facsimile: 650-421-8108                        

7Exhibit10.23TobinTransitionAgreement12-04-2013

Exhibit 10.23
TRANSITION AND SEPARATION AGREEMENT
This Transition and Separation Agreement (the “Agreement”) by and between Matthew B. Tobin (“Executive”) and Codexis, Inc., a Delaware corporation (the “Company”) (the Executive and the Company are collectively referred to herein as the “Parties” or individually as a “Party”), is made effective as of the date Executive signs this Agreement (the “Effective Date”) with reference to the following facts:
A.    Executive’s employment with the Company and status as an employee of the Company and each of its affiliates ended effective upon the Termination Date (as defined below).
B.    Executive and the Company want to end their relationship amicably and also to establish the obligations of the Parties including, without limitation, all amounts due and owing to Executive.
NOW, THEREFORE, in consideration of the mutual covenants and agreements hereinafter set forth, the Parties agree as follows:
		
	1.
	Termination Date.  Executive acknowledges and agrees that his status as an employee of the Company ended effective as of November 15, 2013 (such date, the “Termination Date”).  

		
	2.
	Final Pay and Expenses.  On the Termination Date, Executive acknowledges that Company paid to Executive all accrued but unpaid wages (including, but not limited to, base salary) and the value of all accrued and unused paid-time off earned through the Termination Date, subject to standard payroll deductions and withholdings.  In addition, Executive acknowledges that Company reimbursed Executive for all outstanding expenses incurred prior to the Termination Date which were consistent with the Company’s policies then in effect with respect to travel, entertainment and other business expenses, subject to the Company’s requirements with respect to reporting and documenting such expenses.  Executive is entitled to the payments set forth in this Section 2 regardless of whether Executive executes this Agreement.

		
	3.
	Separation Payments and Benefits.  Subject to Executive signing and delivering to the Company this Agreement prior to 5:00 p.m. (California time) on December 4, 2013 and Executive’s continuing obligations pursuant to this Agreement and that certain Confidential Information, Secrecy and Invention Agreement entered into between Executive and the Company as of May 21, 2003 (the “Confidentiality Agreement”), then within thirty (30) days after the Effective Date, the Company hereby agrees, without admission of any liability, fact or claim, to provide Executive the severance pay and benefits set forth below.  Specifically, the Company and Executive agree as follows:

(a)    Severance Pay.  The Company shall pay Executive an amount equal to $141,636 as a severance payment (the “Severance Payment”).    
(b)    Bonus.  The Company shall pay Executive an amount equal to $63,645, which represents Executive’s pro rata bonus for fiscal year 2013, less required withholding taxes. 
(c)    Healthcare Continuation Coverage.  If Executive elects to receive continued healthcare coverage pursuant to COBRA, the Company shall pay for the premiums for Executive and Executive’s covered dependents during the period commencing on the first day of the first month following the Termination Date through November 30, 2014 (the “COBRA Payment Period”).  The Executive shall notify the Company in writing within five days of becoming eligible for healthcare coverage through other employment, or if he or any of his covered dependents become ineligible for COBRA, during the COBRA Payment Period.  Notwithstanding the previous sentence,  if the Company determines in its sole discretion that it cannot provide the foregoing benefit without potentially violating applicable law (including, without limitation, Section 2716 of the Public Health Service Act), the Company shall in lieu thereof provide to Executive a taxable monthly payment in an amount equal to the monthly COBRA premium that Executive would be required to pay to continue Executive’s and his covered dependents’ group insurance coverages in effect on the Termination Date (which amount shall be based on  the premiums for the first month of COBRA coverage). After the Company ceases to pay the premiums pursuant to this Section 3(c), Executive may, if eligible, elect to continue healthcare coverage at Executive’s expense in accordance with the provisions of COBRA.  
(d)    Taxes.  Executive understands and agrees that all payments and benefits under clauses (a), (b) and (c) of this Section 3 and under Section 4 below will be subject to appropriate tax withholding and other deductions.  To the extent any taxes may be payable by Executive for the payments and benefits provided to him by this Agreement beyond those withheld by the Company, Executive agrees to pay them himself and to indemnify and hold the Company and the other entities released herein harmless for any tax claims or penalties, and associated attorneys’ fees and costs, resulting from any failure by him to make required payments.  
(e)    Executive Outplacement.  The Company shall pay for up to $5,000 in executive career transition services for Executive with Lee Hecht Harrison LLC (“LHH”).  If Executive wishes to engage LHH in these services, he must initiate the transition program with LHH on or before January 31, 2014.
(f)    Sole Separation Benefit.  Executive agrees that the payment and benefits provided by this Section 3 and Section 4 below are not required under the Company’s normal policies and procedures and are provided as a severance payment and benefits solely in connection with this Agreement.  Executive acknowledges and agrees that the payments and benefits referenced in this Section 3 and Section 4 below constitute 

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adequate and valuable consideration, in and of themselves, for the promises contained in this Agreement and the General Release.
(g)    SEC Reporting.  Executive acknowledges that to the extent required by the Securities Exchange Act of 1934, as amended (the “Exchange Act”), he will have continuing obligations under Section 16(a) and 16(b) of the Exchange Act to report his transactions in Company common stock for the six (6) month period following November 15, 2013.  Executive hereby agrees not to undertake, directly or indirectly, any reportable transactions until the end of such six (6)-month period.
		
	4.
	One-Time Separation Payment.  In addition to the payments set forth in Section 3 above, subject to Executive signing and delivering to the Company the General Release of Claims attached as Exhibit A (the “General Release”) hereto, within the thirty (30)-day period immediately following the General Release no longer becoming subject to its revocation as provided in Section 1(c)(iii) thereof and Executive’s continuing obligation pursuant to this Agreement and the Confidentiality Agreement, the Company hereby agrees, without admission of any liability, fact or claim, to pay Executive a one-time separation payment equal to $10,000 (the “Separation Payment”).

		
	5.
	Full Payment.  Executive acknowledges that the payments and arrangements herein shall constitute full and complete satisfaction of any and all amounts properly due and owing to Executive as a result of his employment with the Company and the termination thereof.  Executive further acknowledges that, other than the Confidentiality Agreement, the General Release, that certain Indemnification Agreement between Executive and the Company effective November 12, 2013 (the “Indemnification Agreement”) and each equity award agreement, this Agreement shall supersede each agreement entered into between Executive and the Company regarding Executive’s employment, including, without limitation, Executive’s offer letter agreement with the Company (the “Offer Letter”) and the Change of Control Severance Agreement between Executive and the Company effective November 8, 2012 (the “Change of Control Agreement”), and each such agreement shall be deemed terminated and of no further effect as of the Effective Date.

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	6.
	Equity Awards.  

(a)Each option to purchase shares of the Company’s common stock held by Executive as of the Termination Date that is vested and exercisable on the Termination Date (collectively, the “Vested Stock Options”) shall be exercisable through Executive’s E*Trade account or by following the procedures set forth in Executive’s option agreements, provided that if Executive has not exercised his Vested Stock Options on or before the date occurring three months following the Termination Date (the “Option Termination Date”), Executive’s Vested Stock Options shall automatically terminate and be of no further effect. Executive acknowledges that if he elects to exercise his Vested Stock Options by following the procedures set forth in his option agreements, the Company must receive a duly executed notice of exercise and remuneration in accordance with Executive’s option agreements on or before the Option Termination Date.  
(b)Effective on the Termination Date, (i) all of Executive’s options to purchase shares of Company common stock that are not then fully vested automatically terminated and (ii) all of Executive’s restricted stock units and performance stock units automatically terminated.
		
	7.
	Executive’s Release of the Company.  Executive understands that by agreeing to the release provided by this Section 7, Executive is agreeing not to sue, or otherwise file any claim against, the Company or any of the other Releasees (as defined below) for any reason whatsoever based on anything that has occurred as of the date Executive signs this Agreement.  

(a)    Full Release.  In consideration of the mutual covenants and agreements set forth herein, on behalf of Executive and Executive’s heirs, assigns, executors, administrators, trusts, spouse (current of former), domestic partner, and estate, Executive hereby releases and forever discharges the “Releasees” hereunder, consisting of the Company, and each of its stockholders, affiliates, subsidiaries, predecessors, successors, assigns, agents, directors, officers, partners, employees, and insurers, and all persons acting by, through, under or in concert with them, or any of them, of and from any and all manner of action or actions, cause or causes of action, in law or in equity, suits, debts, liens, contracts, agreements, promises, liability, claims, demands, damages, loss, cost or expense, of any nature whatsoever, known or unknown, fixed or contingent (hereinafter called “Claims”), which Executive now has or may hereafter have against the Releasees, or any of them, by reason of any matter, cause, or thing whatsoever from the beginning of time to the date Executive signs this Agreement, including, without limiting the generality of the foregoing, any Claims arising out of, based upon, or relating to Executive’s hire, employment, remuneration or separation by the Releasees, or any of them, including any Claims arising under Title VII of the Civil Rights Act of 1964, as amended, 42 U.S.C. § 2000, et seq.; Americans with Disabilities Act, as amended, 42 U.S.C. § 12101 et seq.; the Rehabilitation Act of 1973, as amended, 29 U.S.C. § 701 et seq.; Civil Rights Act of 1866, and Civil Rights Act of 1991; 42 U.S.C. § 1981, et seq.; Equal Pay Act, as amended, 29 U.S.C. § 206(d); regulations of the 

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Office of Federal Contract Compliance, 41 C.F.R. Section 60, et seq.; The Family and Medical Leave Act, as amended, 29 U.S.C. § 2601 et seq.; the Fair Labor Standards Act of 1938, as amended, 29 U.S.C. § 201 et seq.; the Employee Retirement Income Security Act, as amended, 29 U.S.C. § 1001 et seq.; the Worker Adjustment and Retraining Notification Act, as amended, 29 U.S.C. § 2101 et seq.; the California Fair Employment and Housing Act, as amended, Cal. Lab.  Code § 12940 et seq.; the California Equal Pay Law, as amended, Cal. Lab.  Code §§ 1197.5(a), 199.5; the Moore-Brown-Roberti Family Rights Act of 1991, as amended, Cal. Gov’t Code §§12945.2, 19702.3; California Labor Code §§ 1101, 1102; the California WARN Act, California Labor Code §§ 1400 et. seq; California Labor Code §§ 1102.5(a), (b); claims for wages under the California Labor Code and any other federal, state or local laws of similar effect.
(b)    Exceptions.  Notwithstanding the generality of the foregoing, Executive does not release the following claims:
		
	(i)
	Claims for unemployment compensation or any state disability insurance benefits pursuant to the terms of applicable state law;

		
	(ii)
	Claims for workers’ compensation insurance benefits under the terms of any worker’s compensation insurance policy or fund of the Company;

		
	(iii)
	Claims to continued participation in certain of the Company’s group benefit plans pursuant to the terms and conditions of COBRA;

		
	(iv)
	Claims for indemnification under California Labor Code Section 2802, the Company’s Certificate of Incorporation, the Company’s Bylaws, the Delaware General Corporation Law or the Indemnification Agreement;

		
	(v)
	Executive’s right to bring to the attention of the Equal Employment Opportunity Commission claims of discrimination; provided, however, that Executive does release Executive’s right to secure any damages for alleged discriminatory treatment; 

		
	(vi)
	Claims arising solely out of Executive’s holdings of Company capital stock as of the date hereof;  

		
	(vii)
	Any other claim that may not be released by private agreement; and

		
	(viii)
	Any other obligation of the Company that cannot be waived as a matter of law.

(c)    California Civil Code Section 1542.  EXECUTIVE ACKNOWLEDGES THAT EXECUTIVE HAS BEEN ADVISED OF AND IS FAMILIAR WITH THE PROVISIONS OF CALIFORNIA CIVIL CODE SECTION 1542, WHICH PROVIDES AS FOLLOWS:

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“A GENERAL RELEASE DOES NOT EXTEND TO CLAIMS WHICH THE CREDITOR DOES NOT KNOW OR SUSPECT TO EXIST IN HIS OR HER FAVOR AT THE TIME OF EXECUTING THE RELEASE, WHICH, IF KNOWN BY HIM OR HER, MUST HAVE MATERIALLY AFFECTED HIS OR HER SETTLEMENT WITH THE DEBTOR.”
BEING AWARE OF SAID CODE SECTION, EXECUTIVE HEREBY EXPRESSLY WAIVES ANY RIGHTS EXECUTIVE MAY HAVE THEREUNDER, AS WELL AS UNDER ANY OTHER STATUTES OR COMMON LAW PRINCIPLES OF SIMILAR EFFECT.
		
	8.
	Non-Disparagement, Transition and Transfer of Company Property.

(a)    Non-Disparagement.  Executive agrees that he shall not disparage, criticize or defame the Company, its affiliates and their respective affiliates, directors, officers, agents, partners, stockholders, employees, products, services, technology or businesses, either publicly or privately.  The Company agrees that it shall not, and it shall instruct its officers and members of its Board of Directors to not, disparage, criticize or defame Executive, either publicly or privately.  Nothing in this Section 8(a) shall have application to any evidence or testimony required by any court, arbitrator or government agency.
(b)    Transition.  Each of the Company and Executive shall use their respective reasonable efforts to cooperate with each other in good faith to facilitate a smooth transition of Executive’s duties to other executive(s) or employees of the Company.
(c)    Transfer of Company Property.  Executive confirms that he has turned over to the Company all files, memoranda, records, and other documents, and any other physical or personal property which are the property of the Company and which he had in his possession, custody or control on or before the Termination Date.  Should Executive discover after the date of this Agreement that he inadvertently failed to return Company property to the Company, Executive agrees to return promptly all such Company property to Company.  Any Company property returned in accordance with the previous sentence will not be deemed to be a breach of this Agreement.
		
	9.
	Executive Representations.  Executive warrants and represents that (a) he has not filed or authorized the filing, and has no intention or plan (as of the date of this Agreement) to file or authorize the filing, of any complaints, charges or lawsuits against the Company or any affiliate of the Company with any governmental agency or court, and that if, unbeknownst to Executive, such a complaint, charge or lawsuit has been filed on his behalf, he will immediately cause it to be withdrawn and dismissed, (b) he has reported all hours worked as of the date Executive signs this Agreement and has been paid all compensation, wages, bonuses, commissions, and/or benefits to which he may be entitled and no other compensation, wages, bonuses, commissions and/or benefits are due to him, except as provided in this Agreement, (c) he has no known workplace injuries or occupational diseases and has been provided and/or has not been denied any leave requested under the Family and Medical Leave Act or any similar state law, 

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(d) the execution, delivery and performance of this Agreement by Executive does not and will not conflict with, breach, violate or cause a default under any agreement, contract or instrument to which Executive is a party or any judgment, order or decree to which Executive is subject, and (e) upon the execution and delivery of this Agreement by the Company and Executive, this Agreement will be a valid and binding obligation of Executive, enforceable in accordance with its terms.
		
	10.
	No Assignment.  Executive warrants and represents that no portion of any of the matters released herein, and no portion of any recovery or settlement to which Executive might be entitled, has been assigned or transferred to any other person, firm or corporation not a party to this Agreement, in any manner, including by way of subrogation or operation of law or otherwise.  If any claim, action, demand or suit should be made or instituted against the Company or any other Releasee because of any actual assignment, subrogation or transfer by Executive, Executive agrees to indemnify and hold harmless the Company and all other Releasees against such claim, action, suit or demand, including necessary expenses of investigation, attorneys’ fees and costs.

		
	11.
	Non-Solicitation.  Without limiting the Confidentiality Agreement, Executive hereby agrees that Executive shall not, at any time during the one (1) year period immediately following the Termination Date, directly or indirectly, either for himself or on behalf of any other person, recruit or otherwise solicit or induce any employee or consultant of the Company to terminate his or her employment or arrangement with the Company, or otherwise change its relationship with the Company.  Notwithstanding the foregoing, nothing herein shall prevent Executive from directly or indirectly hiring any individual who submits a resume or otherwise applies for a position in response to a publicly posted job announcement or otherwise applies for employment with any person with whom Executive may be associated absent any violation of Executive’s obligations pursuant to the preceding sentence.

		
	12.
	Governing Law; Attorney’s Fees.  This Agreement shall be construed and enforced in accordance with, and the rights of the Parties shall be governed by, the laws of the State of California, without regard to any conflicts of laws provisions thereof.  In the event that any provision of this Agreement is ever determined by a court or other applicable tribunal to be void or unenforceable, the remaining provisions of the Agreement shall not be affected and shall remain in full force and effect, to the fullest extent permitted by applicable law.  The prevailing Party in any action to enforce any provisions of this Agreement shall be entitled to an award of costs and reasonable attorneys’ fees in addition to any other relief awarded.

		
	13.
	In the Event of a Claimed Breach.  All controversies, claims and disputes arising out of or relating to Executive’s employment or this Agreement, including without limitation any alleged violation of any contractual terms, shall be resolved (after reasonable informal resolution efforts have failed) by final and binding arbitration before a single neutral arbitrator in San Mateo County, California, in accordance with the applicable dispute resolution rules of the Judicial Arbitration and Mediation Service (“JAMS”). The arbitration shall be commenced by filing a demand for arbitration with JAMS 

7

within 14 days after the filing Party has given written notice of such breach to the other Party.  The arbitrator shall be mutually agreed upon by the Parties or, if the Parties are unable to agree, appointed by JAMS in accordance with its procedures.  The Company shall pay all costs of arbitration, including all administrative and arbitrator fees, that exceed the amount Executive would have incurred had the dispute been filed in California state court in San Mateo County.  Except as provided for in the preceding sentence and as otherwise provided by law, each Party shall bear its own fees, costs and expenses associated with the arbitration, including without limitation attorneys’ fees and expert fees.  Notwithstanding the foregoing, it is acknowledged that it will be impossible to measure in money the damages that would be suffered as a result of any non-compliance with the obligations of Sections 8(a), 8(b), 11, and 15 hereof, and that in the event of a breach of any such provision, an aggrieved Party will be irreparably damaged and will not have an adequate remedy at law.  Any such Party shall, therefore, be entitled to seek injunctive relief in any court of competent jurisdiction, including specific performance, to enforce such obligations, and if any action shall be brought in equity to enforce any of the provisions of Sections 8(a), 8(b), 11 and 15 hereof, neither of the Parties hereto shall raise the defense that there is an adequate remedy at law.
		
	14.
	Miscellaneous.  This Agreement, together with the Confidentiality Agreement, the General Release, the Indemnification Agreement and each equity award agreement, comprise the entire agreement between the Parties with regard to the subject matter hereof and supersedes, in their entirety, any other agreements between Executive and the Company with regard to the subject matter hereof, including, without limitation, the Offer Letter and the Change of Control Agreement.  Executive acknowledges that there are no other agreements, written, oral or implied, and that he may not rely on any prior negotiations, discussions, representations or agreements.  This Agreement may be modified only in writing, and such writing must be signed by both Parties and recited that it is intended to modify this Agreement.  This Agreement may be executed in separate counterparts, each of which is deemed to be an original and all of which taken together constitute one and the same agreement.

		
	15.
	Confidentiality Agreement Obligations.  Executive reaffirms his obligations under the Confidentiality Agreement and agrees to continue to abide by the terms set forth in his Confidentiality Agreement.  Executive confirms that he delivered a signed copy of the termination certificate, which is attached as Exhibit A to the Confidentiality Agreement (the “Termination Certificate”), to Human Resources on or before the Termination Date.  Executive confirms that he understands that the Company will not pay Executive any benefits under this Agreement unless the Company has received such signed Termination Certificate.

		
	16.
	Failure to Comply.  In the event that Executive breaches any of his obligations set forth in this Agreement (including, without limitation, the obligations set forth in Sections 8(a), 8(b), 11 and 15) or as otherwise imposed by law, the Company shall be entitled to stop any payments and/or recover the full benefit paid to Executive under this Agreement and to obtain all other relief provided by law or equity.

8

		
	17.
	Executive’s Cooperation.  Executive shall reasonably cooperate with the Company and its affiliates, upon the Company’s reasonable request, with respect to any internal investigation or administrative, regulatory or judicial proceeding involving matters within the scope of Executive’s duties and responsibilities to the Company during his employment with the Company (including, without limitation, Executive being available to the Company upon reasonable notice for interviews and factual investigations, appearing at the Company’s reasonable request to give testimony without requiring service of a subpoena or other legal process, and turning over to the Company all relevant Company documents which are or may have come into Executive’s possession during his employment); provided, however, that within 30 days of a request by Executive, the Company will reimburse Executive for any reasonable and documented out-of-pocket expenses incurred by Executive for travel or otherwise in connection with any of the above obligations (the “Reimbursable Expenses”).  If Executive is required to spend more than five hours per month providing assistance to the Company under this Section 17, the Company agrees to pay Executive, in addition to the Reimbursable Expenses, at a rate equal to $150 per hour for each hour in excess of five hours per month in which Executive performs such services.

		
	18.
	Unemployment.  It is understood that if Executive files for unemployment benefits with the California Employment Development Department, the Company will not dispute Executive’s claim to such benefits.

Signature Page Follows

9

IN WITNESS WHEREOF, the undersigned have caused this Agreement to be duly executed and delivered as of the date indicated next to their respective signatures below.
	
		
	

Dated:  December 4, 2013
	

/s/Matthew B. Tobin________________  
Matthew B. Tobin

	 
	

CODEXIS, INC.

	

Dated:  December 4, 2013
	

By:   /s/Douglas T. Sheehy   
Douglas Sheehy 
Senior Vice President, General Counsel and Secretary

10

EXHIBIT A

GENERAL RELEASE OF CLAIMS

This General Release of Claims (“Release”) is entered into as of this ___ day of _________________, ____, between Matthew B. Tobin (“Executive”), and Codexis, Inc. (the “Company”) (collectively referred to herein as the “Parties”), effective eight days after Executive’s signature, unless Executive revokes his acceptance as provided in Section 1(c)(iii) below.  Executive is executing this Release in further consideration for the mutual covenants and agreements contained in the Transition and Separation Agreement between Executive and the Company effective as of December ___, 2013 (the “Separation Agreement”).
		
	1.
	General Release of the Company.  Executive understands that by agreeing to this Release, Executive is agreeing not to sue, or otherwise file any claim against, the Company or any of the other Releasees (as defined below) for any reason whatsoever based on anything that has occurred as of the date Executive signs this Release.  

(a)    On behalf of Executive and Executive’s heirs, assigns, executors, administrators, trusts, spouse (current of former), domestic partner, and estate, Executive hereby releases and forever discharges the “Releasees” hereunder, consisting of the Company, and each of its stockholders, affiliates, subsidiaries, predecessors, successors, assigns, agents, directors, officers, partners, employees, and insurers, and all persons acting by, through, under or in concert with them, or any of them, of and from any and all manner of action or actions, cause or causes of action, in law or in equity, suits, debts, liens, contracts, agreements, promises, liability, claims, demands, damages, loss, cost or expense, of any nature whatsoever, known or unknown, fixed or contingent (hereinafter called “Claims”), which Executive now has or may hereafter have against the Releasees, or any of them, by reason of any matter, cause, or thing whatsoever from the beginning of time to the date Executive signs this Release, including, without limiting the generality of the foregoing, any Claims arising out of, based upon, or relating to Executive’s hire, employment, remuneration or separation by the Releasees, or any of them, including any Claims arising under Title VII of the Civil Rights Act of 1964, as amended, 42 U.S.C. § 2000, et seq.; Americans with Disabilities Act, as amended, 42 U.S.C. § 12101 et seq.; the Rehabilitation Act of 1973, as amended, 29 U.S.C. § 701 et seq.; Age Discrimination in Employment Act, as amended, 29 U.S.C. § 621, et seq.; Civil Rights Act of 1866, and Civil Rights Act of 1991; 42 U.S.C. § 1981, et seq.; Equal Pay Act, as amended, 29 U.S.C. § 206(d); regulations of the Office of Federal Contract Compliance, 41 C.F.R. Section 60, et seq.; The Family and Medical Leave Act, as amended, 29 U.S.C. § 2601 et seq.; the Fair Labor Standards Act of 1938, as amended, 29 U.S.C. § 201 et seq.; the Employee Retirement Income Security Act, as amended, 29 U.S.C. § 1001 et seq.; the Worker Adjustment and Retraining Notification Act, as amended, 29 U.S.C. § 2101 et seq.; the California Fair Employment and Housing Act, as amended, Cal. Lab.  Code § 12940 et seq.; the California Equal Pay Law, as amended, Cal. Lab.  Code §§ 1197.5(a), 199.5; the Moore-Brown-Roberti Family Rights Act of 1991, as amended, Cal. Gov’t Code §§12945.2, 19702.3; 

11

California Labor Code §§ 1101, 1102; the California WARN Act, California Labor Code §§ 1400 et. seq; California Labor Code §§ 1102.5(a), (b); claims for wages under the California Labor Code and any other federal, state or local laws of similar effect.
(b)    Notwithstanding the generality of the foregoing, Executive does not release the following claims:
		
	(i)
	Claims for unemployment compensation or any state disability insurance benefits pursuant to the terms of applicable state law;

		
	(ii)
	Claims for workers’ compensation insurance benefits under the terms of any worker’s compensation insurance policy or fund of the Company;

		
	(iii)
	Claims to continued participation in certain of the Company’s group benefit plans pursuant to the terms and conditions of COBRA;

		
	(iv)
	Claims for indemnification under California Labor Code Section 2802, the Company’s Certificate of Incorporation, the Company’s Bylaws, the Delaware General Corporation Law or the Indemnification Agreement (as such term is defined in the Separation Agreement);

		
	(v)
	Executive’s right to bring to the attention of the Equal Employment Opportunity Commission claims of discrimination; provided, however, that Executive does release Executive’s right to secure any damages for alleged discriminatory treatment; 

		
	(vi)
	Claims arising solely out of Executive’s holdings of Company capital stock as of the date hereof;

		
	(vii)
	Any other claim that may not be released by private agreement; and

		
	(viii)
	Any other obligation of the Company that cannot be waived as a matter of law.

(c)    In accordance with the Older Workers Benefit Protection Act of 1990, Executive has been advised of the following:
		
	(i)
	Executive should consult with an attorney before signing this Release;

		
	(ii)
	Executive has been given at least forty (45) days to consider this Release;

		
	(iii)
	Executive has seven (7) days after signing this Release to revoke it.  If Executive wishes to revoke this Release, Executive must deliver notice of Executive’s revocation in writing, no later than 5:00 p.m. on the 7th day following Executive’s execution of this Release to Douglas Sheehy, Senior Vice President, General Counsel and Secretary, 200 Penobscot Drive, Redwood City, California 94063, fax:  (650) 421‐8108.  

12

Executive understands that if he revokes this Release, it will be null and void in its entirety, and he will not be entitled to any payments set forth in Section 4 of the Separation Agreement.
(d)    EXECUTIVE ACKNOWLEDGES THAT EXECUTIVE HAS BEEN ADVISED OF AND IS FAMILIAR WITH THE PROVISIONS OF CALIFORNIA CIVIL CODE SECTION 1542, WHICH PROVIDES AS FOLLOWS:
“A GENERAL RELEASE DOES NOT EXTEND TO CLAIMS WHICH THE CREDITOR DOES NOT KNOW OR SUSPECT TO EXIST IN HIS OR HER FAVOR AT THE TIME OF EXECUTING THE RELEASE, WHICH, IF KNOWN BY HIM OR HER, MUST HAVE MATERIALLY AFFECTED HIS OR HER SETTLEMENT WITH THE DEBTOR.”
BEING AWARE OF SAID CODE SECTION, EXECUTIVE HEREBY EXPRESSLY WAIVES ANY RIGHTS EXECUTIVE MAY HAVE THEREUNDER, AS WELL AS UNDER ANY OTHER STATUTES OR COMMON LAW PRINCIPLES OF SIMILAR EFFECT.
		
	1.
	Executive’s Representations.  Executive represents and warrants that:

(a)     Executive has not filed or authorized the filing, and has no intention or plan (as of the date of this Release) to file or authorize the filing, of any complaints, charges or lawsuits against the Company or any affiliate of the Company with any governmental agency or court;
 (b)     Executive has reported all hours worked as of the date Executive signs this Release and has been paid all compensation, wages, bonuses, commissions, and/or benefits to which he may be entitled and no other compensation, wages, bonuses, commissions and/or benefits are due to him other than those described in Section 3 of the Separation Agreement that will be due to Executive upon satisfaction of the conditions described in Section 3 of the Separation Agreement;
(c)    Executive has no known workplace injuries or occupational diseases and has been provided and/or has not been denied any leave requested under the Family and Medical Leave Act or any similar state law;
		
	(a)
	Executive has returned to the Company all Company property in his possession; 

(b)    Executive has not made any disparaging comments about the Company, nor will Executive do so in the future;
 (f)     the execution, delivery and performance of this Release by Executive does not and will not conflict with, breach, violate or cause a default under any agreement, contract or instrument to which Executive is a party or any judgment, order or decree to which Executive is subject; and

13

 (g)     upon the execution and delivery of this Release by the Company and Executive and expiration of Executive’s revocation rights described in Section 1(c)(iii) of this Release, this Release will be a valid and binding obligation of Executive, enforceable in accordance with its terms
3.    Severability.  The provisions of this Release are severable.  If any provision is held to be invalid or unenforceable, it shall not affect the validity or enforceability of any other provision.

4.    Governing Law.  This Release shall be construed and enforced in accordance with, and the rights of the Parties shall be governed by, the laws of the State of California or, where applicable, United States federal law, in each case, without regard to any conflicts of laws provisions or those of any State other than California.

5.    Miscellaneous.  This Release, together with the Separation Agreement, the Confidentiality Agreement, the Indemnification  Agreement (as each such term is defined in the Separation Agreement) and the equity award agreements, comprise the entire agreement between the Parties with regard to the subject matter hereof and thereof and supersedes, in their entirety, any other agreements between Executive and the Company with regard to the subject matter hereof and thereof, including, without limitation, the Offer Letter and the Change of Control Agreement (as each such term is defined in the Separation Agreement).  This Release may be modified only in writing, and such writing must be signed by both Parties and recited that it is intended to modify this Release.  This Release may be executed in separate counterparts, each of which is deemed to be an original and all of which taken together constitute one and the same agreement.

The Parties have carefully read this Release in its entirety; fully understand and agree to its terms and provisions; and intend and agree that it is final and binding on all Parties.

Signature page follows

14

IN WITNESS WHEREOF, the undersigned have caused this Release to be duly executed and delivered as of the date indicated next to their respective signatures below.
	
		
	

Dated:  ________________
	

   
Matthew B. Tobin   

	 
	

CODEXIS, INC.

	

Dated:  ________________
	

By:      
Douglas Sheehy 
Senior Vice President, General Counsel and Secretary

15

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