Exhibit 10.5

Executive Officers

VERENIUM CORPORATION

2007 EQUITY INCENTIVE PLAN

RESTRICTED STOCK BONUS AGREEMENT

Pursuant to the Restricted Stock Bonus Grant Notice (“Grant Notice”) and this
Restricted Stock Bonus Agreement (collectively, the “Award”) and in
consideration of your past services, Verenium Corporation (the “Company”) has
awarded you a stock bonus under its 2007 Equity Incentive Plan (the “Plan”) for
the number of shares of the Company’s Common Stock subject to the Award as
indicated in the Grant Notice. Defined terms not explicitly defined in this
Restricted Stock Bonus Agreement but defined in the Plan shall have the same
definitions as in the Plan.

The details of your Award are as follows:

1. VESTING. Subject to the limitations contained herein, your Award will vest as
provided in the Grant Notice, provided that vesting will cease upon the
termination of your Continuous Service.

2. NUMBER OF SHARES. The number of shares subject to your Award may be adjusted
from time to time for Capitalization Adjustments, as provided in the Plan.

3. SECURITIES LAW COMPLIANCE. You may not be issued any shares under your Award
unless the shares are either (i) then registered under the Securities Act or
(ii) the Company has determined that such issuance would be exempt from the
registration requirements of the Securities Act. Your Award must also comply
with other applicable laws and regulations governing the Award, and you will not
receive such shares if the Company determines that such receipt would not be in
material compliance with such laws and regulations.

4. RIGHT OF REACQUISITION.

(a) The Company shall have the right to reacquire all or any part of the shares
received pursuant to your Award (a “Reacquisition Right”) as to the shares you
received pursuant to your Award that have not as yet vested in accordance with
the Vesting Schedule on the Grant Notice (“Unvested Shares”) on the following
terms and conditions:

(i) The Company, shall simultaneously with termination of your Continuous
Service automatically reacquire for no consideration all of the Unvested Shares,
unless the Company agrees to waive its Reacquisition Right as to some or all of
the Unvested Shares. Any such waiver shall be exercised by the Company by
written notice to you or your representative (with a copy to the Escrow Holder
as defined below) within ninety (90) days after the termination of your
Continuous Service, and the Escrow Holder may then release to you the number of
Unvested Shares not being reacquired by the Company. If the Company does not
waive its Reacquisition Right as to all of the Unvested Shares, then upon such
termination of your Continuous Service, the Escrow Holder shall transfer to the
Company the number of shares the Company is reacquiring.

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Executive Officers

 

(ii) The Company shall have the right to reacquire Unvested Shares for no
monetary consideration (that is, for $0.00).

(iii) The shares issued under your Award shall be held in escrow pursuant to the
terms of the Joint Escrow Instructions attached to the Grant Notice as
Attachment IV. You agree to execute two (2) Assignment Separate From Certificate
forms (with date and number of shares blank) substantially in the form attached
to the Grant Notice as Attachment III and deliver the same, along with the
certificate or certificates evidencing the shares, for use by the escrow agent
pursuant to the terms of the Joint Escrow Instructions.

(iv) Subject to the provisions of your Award, you shall, during the term of your
Award, exercise all rights and privileges of a shareholder of the Company with
respect to the shares deposited in escrow. You shall be deemed to be the holder
of the shares for purposes of receiving any dividends which may be paid with
respect to such shares and for purposes of exercising any voting rights relating
to such shares, even if some or all of such shares have not yet vested and been
released from the Company’s Reacquisition Right.

(v) If, from time to time, there is any stock dividend, stock split or other
change in the character or amount of any of the outstanding stock of the
corporation the stock of which is subject to the provisions of your Award, then
in such event any and all new, substituted or additional securities to which you
is entitled by reason of your ownership of the shares acquired under your Award
shall be immediately subject to the Reacquisition Right with the same force and
effect as the shares subject to this Reacquisition Right immediately before such
event.

5. CHANGE-IN-CONTROL.

(a) If a Change in Control occurs and as of within one (1) month prior to, or
within thirteen (13) months after, the effective time of such Change in Control
your Continuous Service terminates due to an involuntary termination (not
including death or Disability) without Cause or due to a voluntary termination
with Good Reason, then, as of the date of termination of Continuous Service, the
vesting of your Award shall be accelerated in full.

(b) “Good Reason” means that one or more of the following are undertaken by the
Company without your express written consent: (i) (A) a change in your status,
title, position or responsibilities (including reporting responsibilities) which
represents an adverse change from your status, title, position or
responsibilities as in effect at any time within ninety (90) days preceding the
date of a Change in Control or at any time thereafter; (B) the assignment to you
of any duties or responsibilities which are inconsistent with your status,
title, position or responsibilities as in effect at any time within ninety
(90) days preceding the date of a Change in Control or at any time thereafter;
or (C) any removal of you from or failure to reappoint or reelect you to any of
such offices or positions, except in connection with the termination of your
Continuous Service for Cause, as a result of your Disability or death or by you
other than as a result of voluntary termination with Good Reason; (ii) a
reduction in your annual base compensation or any failure to pay you any
compensation or benefits to which you are entitled within five (5) days of the
date due; (iii) the Company’s requiring you to relocate to any place outside a
forty (40) mile radius of your current work site, except for reasonably required
travel

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Executive Officers

 

on the business of the Company or its Affiliates which is not materially greater
than such travel requirements prior to the Change in Control; (iv) the failure
by the Company to (A) continue in effect (without reduction in benefit level
and/or reward opportunities) any material compensation or employee benefit plan
in which you were participating at any time within ninety (90) days preceding
the date of a Change in Control or at any time thereafter, unless such plan is
replaced with a plan that provides substantially equivalent compensation or
benefits to you, or (B) provide you with compensation and benefits, in the
aggregate, at least equal (in terms of benefit levels and/or reward
opportunities) to those provided for under each other employee benefit plan,
program and practice in which you were participating at any time within ninety
(90) days preceding the date of a Change in Control or at any time thereafter;
(v) any material breach by the Company of any provision of an agreement between
the Company and you, whether pursuant to the Plan, this Agreement or otherwise,
other than a breach which is cured by the Company within fifteen (15) days
following notice by you of such breach; or (vi) the failure of the Company to
obtain an agreement, satisfactory to you, from any successors and assigns to
assume and agree to perform the obligations created under the Plan or this
Agreement.

(c) If any payment or benefit you would receive pursuant to a Change in Control
from the Company or otherwise (“Payment”) would (i) constitute a “parachute
payment” within the meaning of Section 280G of the Code, and (ii) but for this
sentence, be subject to the excise tax imposed by Section 4999 of the Code (the
“Excise Tax”), then such Payment shall be equal to the Reduced Amount. The
“Reduced Amount” shall be either (x) the largest portion of the Payment that
would result in no portion of the Payment being subject to the Excise Tax or
(y) the largest portion, up to and including the total, of the Payment,
whichever amount, after taking into account all applicable federal, state and
local employment taxes, income taxes, and the Excise Tax (all computed at the
highest applicable marginal rate), results in your receipt, on an after-tax
basis, of the greater amount of the Payment notwithstanding that all or some
portion of the Payment may be subject to the Excise Tax. If a reduction in
payments or benefits constituting “parachute payments” is necessary so that the
Payment equals the Reduced Amount, reduction shall occur in the following order
unless you elect in writing a different order (provided, however, that such
election shall be subject to Company approval if made on or after the effective
date of the event that triggers the Payment): reduction of cash payments;
cancellation of accelerated vesting of Stock Awards; reduction of employee
benefits. In the event that acceleration of vesting of Stock Award compensation
is to be reduced, such acceleration of vesting shall be cancelled in the reverse
order of the date of grant of your Stock Awards (i.e., earliest granted Stock
Award cancelled last) unless you elect in writing a different order for
cancellation.

The accounting firm engaged by the Company for general audit purposes as of the
day prior to the effective date of the Change in Control shall perform the
foregoing calculations. If the accounting firm so engaged by the Company is
serving as accountant or auditor for the individual, entity or group effecting
the Change in Control, the Company shall appoint a nationally recognized
accounting firm to make the determinations required hereunder. The Company shall
bear all expenses with respect to the determinations by such accounting firm
required to be made hereunder.

The accounting firm engaged to make the determinations hereunder shall provide
its calculations, together with detailed supporting documentation, to you and
the Company

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Executive Officers

 

within fifteen (15) calendar days after the date on which your right to a
Payment is triggered (if requested at that time by you or the Company) or such
other time as requested by you or the Company. If the accounting firm determines
that no Excise Tax is payable with respect to a Payment, either before or after
the application of the Reduced Amount, it shall furnish you and the Company with
an opinion reasonably acceptable to you that no Excise Tax will be imposed with
respect to such Payment. Any good faith determinations of the accounting firm
made hereunder shall be final, binding and conclusive upon you and the Company.

Notwithstanding any reduction described in this subsection, the IRS determines
that you are liable for the Excise Tax as a result of the receipt of the payment
of benefits as described above, then you shall be obligated to pay back to the
Company, within thirty (30) days after a final IRS determination or in the event
that you challenge the final IRS determination, a final judicial determination,
a portion of the payment equal to the “Repayment Amount.” The Repayment Amount
with respect to the payment of benefits shall be the smallest such amount, if
any, as shall be required to be paid to the Company so that your net after-tax
proceeds with respect to any payment of benefits (after taking into account the
payment of the Excise Tax and all other applicable taxes imposed on such
payment) shall be maximized. The Repayment Amount with respect to the payment of
benefits shall be zero if a Repayment Amount of more than zero would not result
in your net after-tax proceeds with respect to the payment of such benefits
being maximized. If the Excise Tax is not eliminated pursuant to this paragraph,
you shall pay the Excise Tax.

Notwithstanding any other provision of this subsection 5(c), if (i) there is a
reduction in the payment of benefits as described in this subsection, (ii) the
IRS later determines that you are liable for the Excise Tax, the payment of
which would result in the maximization of your net after-tax proceeds
(calculated as if your benefits had not previously been reduced), and (iii) you
pay the Excise Tax, then the Company shall pay to you those benefits which were
reduced pursuant to this subsection contemporaneously or as soon as
administratively possible after you pay the Excise Tax so that your net
after-tax proceeds with respect to the payment of benefits is maximized.

If you either (i) bring any action to enforce rights pursuant to this subsection
5(c), or (ii) defend any legal challenge to your rights hereunder, you shall be
entitled to recover attorneys’ fees and costs incurred in connection with such
action, regardless of the outcome of such action; provided, however, that in the
event such action is commenced by you, the court finds the claim was brought in
good faith.

6. RESTRICTIVE LEGENDS. The shares issued under your Award shall be endorsed
with appropriate legends determined by the Company.

7. AWARD NOT A SERVICE CONTRACT. Your Award is not an employment or service
contract, and nothing in your Award shall be deemed to create in any way
whatsoever any obligation on your part to continue in the employ of the Company
or an Affiliate, or on the part of the Company or an Affiliate to continue your
employment. In addition, nothing in your Award shall obligate the Company or an
Affiliate, their respective shareholders, boards of directors, Officers or
Employees to continue any relationship that you might have as a Director or
Consultant for the Company or an Affiliate.

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Executive Officers

 

8. WITHHOLDING OBLIGATIONS.

(a) At the time your Award is made, or at any time thereafter as requested by
the Company, you hereby authorize withholding from payroll and any other amounts
payable to you, and otherwise agree to make adequate provision for any sums
required to satisfy the federal, state, local and foreign tax withholding
obligations of the Company or an Affiliate, if any, which arise in connection
with your Award.

(b) Unless the tax withholding obligations of the Company and/or any Affiliate
are satisfied, the Company shall have no obligation to issue a certificate for
such shares or release such shares from any escrow provided for herein.

9. TAX CONSEQUENCES. The acquisition and vesting of the shares may have adverse
tax consequences to you that may avoided or mitigated by filing an election
under Section 83(b) of the Internal Revenue Code, as amended (the “Code”). Such
election must be filed within thirty (30) days after the date of your Award. YOU
ACKNOWLEDGE THAT IT IS YOUR OWN RESPONSIBILITY, AND NOT THE COMPANY’S, TO FILE A
TIMELY ELECTION UNDER CODE SECTION 83(B), EVEN IF YOU REQUEST THE COMPANY TO
MAKE THE FILING ON YOUR BEHALF.

10. NOTICES. Any notices provided for in your Award or the Plan shall be given
in writing and shall be deemed effectively given upon receipt or, in the case of
notices delivered by the Company to you, five (5) days after deposit in the
United States mail, postage prepaid, addressed to you at the last address you
provided to the Company.

11. MISCELLANEOUS.

(a) The rights and obligations of the Company under your Award shall be
transferable to any one or more persons or entities, and all covenants and
agreements hereunder shall inure to the benefit of, and be enforceable by the
Company’s successors and assigns. Your rights and obligations under your Award
may only be assigned with the prior written consent of the Company.

(b) You agree upon request to execute any further documents or instruments
necessary or desirable in the sole determination of the Company to carry out the
purposes or intent of your Award.

(c) You acknowledge and agree that you have reviewed your Award in its entirety,
have had an opportunity to obtain the advice of counsel prior to executing and
accepting your Award and fully understand all provisions of your Award.

12. GOVERNING PLAN DOCUMENT. Your Award is subject to all the provisions of the
Plan, the provisions of which are hereby made a part of your Award, and is
further subject to all interpretations, amendments, rules and regulations which
may from time to time be promulgated and adopted pursuant to the Plan. In the
event of any conflict between the provisions of your Award and those of the
Plan, the provisions of the Plan shall control.

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JOINT ESCROW INSTRUCTIONS

[Date]

Corporate Secretary

Verenium Corporation

4955 Directors Place

San Diego, CA 92121

Dear Sir/Madam:

As Escrow Agent for both Verenium Corporation, a Delaware corporation (the
“Company”), and the undersigned recipient of stock of the Company (“Recipient”),
you are hereby authorized and directed to hold the documents delivered to you
pursuant to the terms of that certain Restricted Stock Bonus Grant Notice (the
“Grant Notice”), dated                              to which a copy of these
Joint Escrow Instructions is attached as Attachment IV, and pursuant to the
terms of that certain Restricted Stock Bonus Agreement (“Agreement”), which is
Attachment I to the Grant Notice, in accordance with the following instructions:

1. In the event Recipient ceases to render services to the Company or an
affiliate of the Company during the vesting period set forth in the Grant
Notice, the Company or its assignee will give to Recipient and you a written
notice specifying that the shares of stock shall be transferred to the Company.
Recipient and the Company hereby irrevocably authorize and direct you to close
the transaction contemplated by such notice in accordance with the terms of said
notice.

2. At the closing you are directed (a) to date any stock assignments necessary
for the transfer in question, (b) to fill in the number of shares being
transferred, and (c) to deliver same, together with the certificate evidencing
the shares of stock to be transferred, to the Company.

3. Recipient irrevocably authorizes the Company to deposit with you any
certificates evidencing shares of stock to be held by you hereunder and any
additions and substitutions to said shares as specified in the Grant Notice.
Recipient does hereby irrevocably constitute and appoint you as Recipient’s
attorney-in-fact and agent for the term of this escrow to execute with respect
to such securities and other property all documents of assignment and/or
transfer and all stock certificates necessary or appropriate to make all
securities negotiable and complete any transaction herein contemplated.

4. This escrow shall terminate upon vesting of the shares or upon the earlier
return of the shares to the Company.

5. If at the time of termination of this escrow you should have in your
possession any documents, securities, or other property belonging to Recipient,
you shall deliver all of same to any pledgee entitled thereto or, if none, to
Recipient and shall be discharged of all further obligations hereunder.

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6. Your duties hereunder may be altered, amended, modified or revoked only by a
writing signed by all of the parties hereto.

7. You shall be obligated only for the performance of such duties as are
specifically set forth herein and may rely and shall be protected in relying or
refraining from acting on any instrument reasonably believed by you to be
genuine and to have been signed or presented by the proper party or parties or
their assignees. You shall not be personally liable for any act you may do or
omit to do hereunder as Escrow Agent or as attorney-in-fact for Recipient while
acting in good faith and any act done or omitted by you pursuant to the advice
of your own attorneys shall be conclusive evidence of such good faith.

8. You are hereby expressly authorized to disregard any and all warnings given
by any of the parties hereto or by any other person or corporation, excepting
only orders or process of courts of law, and are hereby expressly authorized to
comply with and obey orders, judgments or decrees of any court. In case you obey
or comply with any such order, judgment or decree of any court, you shall not be
liable to any of the parties hereto or to any other person, firm or corporation
by reason of such compliance, notwithstanding any such order, judgment or decree
being subsequently reversed, modified, annulled, set aside, vacated or found to
have been entered without jurisdiction.

9. You shall not be liable in any respect on account of the identity, authority
or rights of the parties executing or delivering or purporting to execute or
deliver the Grant Notice or any documents or papers deposited or called for
hereunder.

10. You shall not be liable for the outlawing of any rights under any statute of
limitations with respect to these Joint Escrow Instructions or any documents
deposited with you.

11. You shall be entitled to employ such legal counsel, including but not
limited to Cooley Godward Kronish LLP, and other experts as you may deem
necessary properly to advise you in connection with your obligations hereunder,
may rely upon the advice of such counsel, and may pay such counsel reasonable
compensation therefor.

12. Your responsibilities as Escrow Agent hereunder shall terminate if you shall
cease to be Secretary of the Company or if you shall resign by written notice to
each party. In the event of any such termination, the Company may appoint any
officer or assistant officer of the Company as successor Escrow Agent and
Recipient hereby confirms the appointment of such successor or successors as his
attorney-in-fact and agent to the full extent of your appointment.

13. If you reasonably require other or further instruments in connection with
these Joint Escrow Instructions or obligations in respect hereto, the necessary
parties hereto shall join in furnishing such instruments.

14. It is understood and agreed that should any dispute arise with respect to
the delivery and/or ownership or right of possession of the securities, you may
(but are not obligated to) retain in your possession without liability to anyone
all or any part of said securities until such dispute shall have been settled
either by mutual written agreement of the parties concerned or by a final order,
decree or judgment of a court of competent jurisdiction after the time for
appeal has expired and no appeal has been perfected, but you shall be under no
duty whatsoever to institute or defend any such proceedings.

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15. Any notice required or permitted hereunder shall be given in writing and
shall be deemed effectively given upon personal delivery or upon deposit in any
United States Post Box, by registered or certified mail with postage and fees
prepaid, addressed to each of the other parties hereunto entitled at the
following addresses, or at such other addresses as a party may designate by ten
(10) days’ written notice to each of the other parties hereto:

 

  COMPANY:      Verenium Corporation           4955 Directors Place          
San Diego, CA 92121           Attn: * General Counsel / Chief Financial Officer
  RECIPIENT:     

 

         

 

         

 

         

 

     ESCROW AGENT:      Verenium Corporation           4955 Directors Place     
     San Diego, CA 92121           Attn: Corporate Secretary   

16. By signing these Joint Escrow Instructions you become a party hereto only
for the purpose of said Joint Escrow Instructions; you do not become a party to
the Grant Notice.

17. This instrument shall be binding upon and inure to the benefit of the
parties hereto, and their respective successors and permitted assigns. It is
understood and agreed that references to “you” or “your” herein refer to the
original Escrow Agent and to any and all successor Escrow Agents. It is
understood and agreed that the Company may at any time or from time to time
assign its rights under the Grant Notice and these Joint Escrow Instructions in
whole or in part.

 

Very truly yours, VERENIUM CORPORATION

By:

 

 

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RECIPIENT

 

 

Name:  

 

 

 

ESCROW AGENT:

   

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ASSIGNMENT SEPARATE FROM CERTIFICATE

FOR VALUE RECEIVED and pursuant to that certain Restricted Stock Bonus Grant
Notice and Restricted Stock Bonus Agreement (the “Award”), [Participant’s Name]
hereby sells, assigns and transfers unto Verenium Corporation, a Delaware
corporation (“Assignee”)                                                  
(                    ) shares of the common stock of the Assignee, standing in
the undersigned’s name on the books of said corporation represented by
Certificate No.          herewith and do hereby irrevocably constitute and
appoint                                          as attorney-in-fact to transfer
the said stock on the books of the within named Company with full power of
substitution in the premises. This Assignment may be used only in accordance
with and subject to the terms and conditions of the Award, in connection with
the reacquisition of shares of Common Stock of the Corporation issued to the
undersigned pursuant to the Award, and only to the extent that such shares
remain subject to the Corporation’s Reacquisition Right under the Award.

 

Dated:  

 

 

Signature:  

 

[Participant’s Name], Recipient

[INSTRUCTION: Please do not fill in any blanks other than the signature line.
The purpose of this Assignment is to enable the Company to exercise its
Reacquisition Right set forth in the Award without requiring additional
signatures on your part.]