<PAGE>
Exhibit 3.1
AMENDED AND RESTATED
CERTIFICATE OF INCORPORATION
OF
CATALYTICA ENERGY SYSTEMS, INC.
Article I. Name
The name of the corporation is Catalytica Energy Systems, Inc. (the
"Corporation").
Article II. Registered Office and Registered Agent
The address of the registered office of the Corporation in the State of
Delaware is Corporation Trust Center, 1209 Orange Street, City of Wilmington,
County of New Castle, Delaware 19801. The name of its registered agent at the
foregoing address is The Corporation Trust Company.
Article III. Purpose
The nature of the business or purposes to be conducted or promoted is to
engage in any lawful act or activity for which corporations may be organized
under the General Corporation Law of the State of Delaware, as amended from time
to time (the "DGCL").
Article IV. Authorized Capital
1. Total Capital Authorized.
The total number of shares of all classes of capital stock which the
Corporation shall have authority to issue is 75,000,000 shares, comprised of
70,000,000 shares of Common Stock with a par value of $0.001 per share (the
"Common Stock") and 5,000,000 shares of Preferred Stock with a par value of
$0.001 per share (the "Preferred Stock").
2. Preferred Stock.
The Preferred Stock may be issued in one or more series at such time or
times and for such consideration or considerations as the Board of Directors of
the Corporation may determine. Each series shall be so designated as to
distinguish the shares thereof from the shares of all other series and classes.
Except as may be expressly provided in this Amended and Restated Certificate of
Incorporation, including any certificate of
<PAGE>
designations for a series of Preferred Stock, different series of Preferred
Stock shall not be construed to constitute different classes of shares for the
purpose of voting by classes.
The Board of Directors of the Corporation is expressly authorized, subject
to the limitations prescribed by law and the provisions of this Amended and
Restated Certificate of Incorporation, to provide for the issuance of all or any
shares of Preferred Stock, in one or more series, each with such designations,
preferences, voting powers (or no voting powers), relative, participating,
optional or other special rights and privileges and such qualifications,
limitations or restrictions thereof as shall be stated in the resolution or
resolutions adopted by the Board of Directors to create such series, and a
certificate of designations setting forth a copy of said resolution or
resolutions shall be filed in accordance with the DGCL. The authority of the
Board of Directors with respect to each series of Preferred Stock shall include
without limitation of the foregoing the right to specify the number of shares of
that series and to authorize an increase or decrease in such number of shares
and the right to provide that the shares of each series may be: (a) subject to
redemption at such time or times and at such price or prices; (b) entitled to
receive dividends (which may be cumulative or non-cumulative) at such rates, on
such conditions, and at such times, and payable in preference to, or in relation
to, the dividends payable on any other class or classes or any other series; (c)
entitled to such rights upon the dissolution of, or upon any distribution of the
assets of, the Corporation; (d) convertible into, or exchangeable for, shares of
any other class or classes of stock, or of any other series of the same or any
other class or classes of stock of the Corporation at such price or prices or at
such rates of exchange and with such adjustments, if any; (e) entitled to the
benefit of such limitations, if any, on the issuance of additional shares of
such series or shares of any other series of Preferred Stock; or (f) entitled to
such other preferences, powers, qualifications, rights and privileges, all as
the Board of Directors of the Corporation may deem advisable and as are not
inconsistent with law and the provisions of this Amended and Restated
Certificate of Incorporation. The number of authorized shares of Preferred Stock
may be increased or decreased (but not below the number of shares thereof then
outstanding) by the affirmative vote of the holders of a majority of the shares
of Common Stock, without a vote of the holders of the Preferred Stock, or of any
series thereof, unless a vote of such holder is required pursuant to the terms
of any Preferred Stock designation.
Upon the filing of this Amended and Restated Certificate of Incorporation
each issued and outstanding share of Preferred Stock shall be converted into one
share of Common Stock, par value per share of $0.001.
Article V. Rights, Preferences, Privileges and Restrictions of Capital Stock
All preferences, voting powers, relative, participating, optional or other
special rights and privileges, and restrictions of the Common Stock are
expressly made subject and subordinate to those that may be fixed with respect
to any shares of Preferred Stock. The preferences, voting powers, relative,
participating, optional or other special rights
2
<PAGE>
and privileges, and restrictions granted to or imposed upon the shares of Common
Stock or the holders thereof are as follows:
1. General Rights, Preferences, Privileges and Restrictions.
Except as otherwise set forth below in this Article V, the powers,
preferences and relative participating, optional or other special rights and
qualifications, limitations or restrictions of the Common Stock shall be
identical in all respects.
2. Dividends.
Subject to any other provisions of this Amended and Restated Certificate of
Incorporation and the preferential rights of the holders of Preferred Stock, if
any, holders of Common Stock and Stock shall be entitled to receive dividends
and other distributions in cash, stock or property of the Corporation as may be
declared thereon by the Board of Directors of the Corporation from time to time
out of assets or funds of the Corporation legally available therefore.
3. Voting Rights.
(a) At every meeting of the stockholders of the Corporation every holder of
Common Stock shall be entitled to one vote in person or by proxy for each share
of Common Stock standing in the stockholder's name on the transfer books of the
Corporation.
(b) The provisions of this Amended and Restated Certificate of
Incorporation shall not be modified, revised, altered or amended, repealed or
rescinded in whole or in part, without the approval of a majority of the votes
entitled to be cast by the holders of the Common Stock.
(c) Notwithstanding the foregoing, except as otherwise required by law,
holders of Common Stock shall not be entitled to vote on any amendment to the
Amended and Restated Certificate of Incorporation of the Corporation (including
any certificate of designations relating to any series of Preferred Stock) that
relates solely to the terms of one or more outstanding series of Preferred Stock
if the holders of the affected series are entitled, either separately or
together as a class with the holders of one or more other series, to vote
thereon pursuant to the Amended and Restated Certificate of Incorporation of the
Corporation (including any certificate of designations relating to any series of
Preferred Stock).
(d) Holders of stock of any class or series of the Corporation shall not be
entitled to cumulate their votes for the election of directors or any other
matter submitted to a vote of the stockholders. If Section 2115 of the
California General Corporation Law applies to the Corporation and if cumulative
voting is required by Section 301.5 of the
3
<PAGE>
California General Corporation Law, each holder shall be entitled to as many
votes as shall equal the number of votes which (except for this provision as to
cumulative voting) the holder would be entitled to cast for the election of
directors with respect to the holder's shares of stock multiplied by the number
of directors to be elected by the holder, and the holder may cast all of their
votes for a single director or may distribute them among the number of directors
to be voted for, or for any two or more of them as the holder may see fit, so
long as the name of the candidate for director shall have been placed in
nomination prior to the voting and the stockholder, or any other holder of the
same class or series of stock, has given notice at the meeting prior to the
voting of the intention to cumulate votes.
4. Dissolution, Liquidation or Winding Up.
In the event of any dissolution, liquidation or winding up of the affairs
of the Corporation, whether voluntary or involuntary, after distribution in full
of the preferential amounts, if any, to be distributed to the holders of
Preferred Stock, if any, the assets and funds of the Corporation shall be
distributed pro rata to the holders of Common Stock based on the number of
shares of Common Stock held by them.
Article VI. Perpetual Existence
The Corporation shall have perpetual existence.
Article VII. Section 203 Inapplicable
In accordance with Section 203(b)(3) of the DGCL, the Corporation expressly
elects not to be governed by Section 203 of the DGCL.
Article VIII. Special Meetings of Stockholders
Special meetings of stockholders of the Corporation, for any purpose or
purposes, unless otherwise prescribed by statute or by this Amended and Restated
Certificate of Incorporation, shall only be called by the Chairman of the Board
or the President or Secretary of the Corporation, at the request in writing of
all members of the Board of Directors, or at the request in writing of
stockholders owning at least 75% of the total voting power of the entire capital
stock of the Corporation issued and outstanding and entitled to vote. Any
request for a special meeting of stockholders shall state the purpose or
purposes of the proposed special meeting of stockholders.
Article IX. Additional Authority
In furtherance and not in limitation of the powers conferred by the laws of
the State of Delaware:
4
<PAGE>
1. Board Authority.
The Board of Directors of the Corporation is expressly authorized:
(a) To make, alter or repeal the bylaws of the Corporation.
(b) To authorize and cause to be executed mortgages and liens upon the real
and personal property of the Corporation.
(c) To set apart out of any of the funds of the Corporation available for
dividends a reserve or reserves for any proper purpose and to abolish any
reserve in the manner in which it was created.
(d) By a majority of the whole board, to designate one or more committees,
each committee to consist of one or more of the directors of the Corporation.
The board may designate one or more directors as alternate members of any
committee, who may replace any absent or disqualified member of any committee.
The bylaws may provide that in the absence or disqualification of a member of a
committee, the member or members thereof present at any meeting and not
disqualified from voting, whether or not constituting a quorum, may unanimously
appoint another member of the Board of Directors to act at the meeting in the
place of any absent or disqualified member. Any committee, to the extent
provided in the resolution of the Board of Directors, or in the bylaws of the
Corporation, shall have and may exercise all the powers and authority of the
Board of Directors in the management of the business and affairs of the
Corporation, and may authorize the seal of the Corporation to be affixed to all
papers which may require it; but no committee shall have the power or authority
in reference to amending the Amended and Restated Certificate of Incorporation,
adopting an agreement of merger or consolidation under Sections 251 or 252 of
the DGCL, recommending to the stockholders the sale, lease or exchange of all or
substantially all of the Corporation's property and assets, recommending to the
stockholders a dissolution of the Corporation or a revocation of a dissolution,
or amending the bylaws of the Corporation. Unless the bylaws or a resolution of
the Board of Directors expressly so provides, no committee shall have the power
or authority to declare a dividend, to authorize the issuance of stock, or to
adopt a certificate of ownership and merger pursuant to Section 253 of the DGCL.
(e) When and as authorized by the stockholders in accordance with statute,
to sell, lease or exchange all or substantially all of the property and assets
of the Corporation, including its good will and its corporate franchises, upon
terms and conditions and for consideration which may consist in whole or in part
of money or property including shares of stock in, and/or other securities of,
any other corporation or corporations, as the Board of Directors shall deem
expedient and in the best interests of the Corporation.
5
<PAGE>
2. Election of Directors.
The election of directors need not be by written ballot unless the bylaws
of the Corporation so provide.
3. Corporate Records.
The books of the Corporation may be kept at any place within or without the
State of Delaware as the bylaws of the Corporation may provide or as may be
designated from time to time by the Board of Directors of the Corporation.
Article X. No Liability
A director of the Corporation shall not be personally liable to the
Corporation or its stockholders for monetary damages for breach of fiduciary
duty as a director, except for liability (a) for any breach of the director's
duty of loyalty to the Corporation or its stockholders, (b) for acts or
omissions not in good faith or which involve intentional misconduct or a knowing
violation of law, (c) under Section 174 of the DGCL, or (d) for any transaction
from which the director derived any improper personal benefit. If the DGCL is
amended after the date of filing of this Amended and Restated Certificate of
Incorporation to authorize corporate action further eliminating or limiting the
personal liability of directors, then the liability of a director of the
Corporation shall be eliminated or limited to the fullest extent permitted by
the DGCL, as so amended.
Any repeal or modification of the foregoing paragraph shall not adversely
affect any right or protection of a director of the Corporation existing at the
time of the repeal or modification.
Article XI. Indemnification
1. Right To Indemnification.
Each person who was or is made a party or is threatened to be made a party
to or is involved in any action, suit or Proceeding, whether civil, criminal,
administrative or investigative ("Proceeding"), by reason of the fact that he or
she or a person of whom he or she is the legal representative, is or was a
director or officer, employee or agent of the Corporation or is or was serving
at the request of the Corporation as a director or officer, employee or agent of
another corporation, or of a partnership, joint venture, trust or other
enterprise, including service with respect to employee benefit plans, whether
the basis of the Proceeding is alleged action in an official capacity as a
director, officer, employee or agent or in any other capacity while serving as a
director, officer, employee or agent, shall be indemnified and held harmless by
the Corporation to the fullest extent authorized by the DGCL, as the same exists
or may hereafter be amended, (but, in the case of any amendment, only to the
extent that the amendment permits the Corporation to provide
6
<PAGE>
broader indemnification rights than the DGCL permitted the Corporation to
provide prior to the amendment) against all expenses, liability and loss
including attorneys' fees, judgments, fines, ERISA excise taxes or penalties and
amounts paid or to be paid in settlement) reasonably incurred or suffered by the
person in connection therewith and the indemnification shall continue as to a
person who has ceased to be a director, officer, employee or agent and shall
inure to the benefit of his or her heirs, executors and administrators;
provided, however, that the Corporation shall indemnify a person seeking
indemnity in connection with an action, suit or Proceeding (or part thereof)
initiated by the person only if the action, suit or Proceeding (or part thereof)
was authorized by the Board of Directors of the Corporation. The right to
indemnification shall be a contract right and shall include the right to be paid
by the Corporation expenses incurred in defending a Proceeding in advance of its
final disposition; provided, however, that the payment of expenses incurred by a
director or officer of the Corporation in his or her capacity as a director or
officer (and not in any other capacity in which service was or is rendered by
the person while a director or officer, including, without limitation, service
to an employee benefit plan) in advance of the final disposition of the
Proceeding, shall be made only upon delivery to the Corporation of an
undertaking, by or on behalf of the director or officer, to repay all amounts
advanced if it should be determined ultimately that the director or officer is
not entitled to be indemnified under this Article or otherwise.
2. Right of Claimant to Bring Suit.
If a claim under paragraph 1 of Article XI is not paid in full by the
Corporation within 90 days after a written claim has been received by the
Corporation, the claimant may at any time thereafter bring suit against the
Corporation to recover the unpaid amount of the claim and, if successful in
whole or in part, the claimant shall be entitled to be paid also the expense of
prosecuting the claim. It shall be a defense to any action for recovery (other
than an action brought to enforce a claim for expenses incurred in defending any
Proceeding in advance of its final disposition where the required undertaking,
if any, has been tendered to the Corporation) that the claimant has not met the
standards of conduct which make it permissible under the DGCL for the
Corporation to indemnify the claimant for the amount claimed, but the burden of
proving this defense shall be on the Corporation. Neither the failure of the
Corporation (including its Board of Directors, independent legal counsel or its
stockholders) to have made a determination prior to the commencement of the
action for recovery that indemnification of the claimant is proper in the
circumstances because he or she has met the applicable standard of conduct set
forth in the DGCL, nor an actual determination by the Corporation (including its
Board of Directors, independent legal counsel or its stockholders) that the
claimant has not met the applicable standard of conduct, shall be a defense to
the action or create a presumption that the claimant has not met the applicable
standard of conduct.
7
<PAGE>
3. Non-Exclusivity of Rights.
The rights conferred on any person by paragraphs 1 and 2 of Article XI
shall not be exclusive of any other right which the persons may have or
hereafter acquire under any statute, provision of the Amended and Restated
Certificate of Incorporation, bylaw, agreement, vote of stockholders or
disinterested directors or otherwise.
4. Insurance.
The Corporation may maintain insurance, at its expense, to protect itself
and any director, officer, employee or agent of the Corporation or another
corporation, partnership, joint venture, trust or other enterprise against any
expense, liability or loss, whether or not the Corporation would have the power
to indemnify the person against the expense, liability or loss under the DGCL.
5. Miscellaneous.
(a) Any repeal or modification of Article XI shall not in any way diminish
any rights to indemnification of such director, officer, employee or agent or
the obligations of the Corporation arising hereunder with respect to any action,
suit or proceeding arising out of, or relating to, any actions, transactions or
facts occurring prior to the final adoption of such modification or repeal.
(b) To the extent that any director, officer, employee or agent of the
Corporation is by reason of such position, or a position with another entity at
the request of the Corporation, a witness in any action, suit or proceeding, he
or she shall be indemnified against all costs and expenses actually and
reasonably incurred by him or her or on his or her behalf in connection
therewith.
(c) The Corporation may enter into agreements with any director, officer,
employee or agent of the Corporation providing for indemnification to the full
extent permitted by Delaware law.
(d) If this Article XI or any portion hereof shall be invalidated on any
ground by any court of competent jurisdiction, then the Corporation shall
nevertheless indemnify each person entitled to indemnification under the first
paragraph of this Article XI as to all expense, liability and loss (including
attorneys' fees, judgments, fines, taxes or penalties and amounts paid or to be
paid in settlement) actually and reasonably incurred or suffered by such person
and for which indemnification is available to such person pursuant to Article XI
to the full extent permitted by any applicable portion of this Article XI that
shall not have been invalidated and to the full extent permitted by applicable
law.
8
<PAGE>
Article XII. Reservation of Rights
The Corporation reserves the right to amend or repeal any provision
contained in this Amended and Restated Certificate of Incorporation, in the
manner now or hereafter prescribed by statute, and all rights conferred upon a
stockholder herein are granted expressly subject to this reservation.
9
