RESTATED CERTIFICATE OF INCORPORATION
 
                                       OF
 
                                 NITROMED, INC.
 
                        --------------------------------
 
                     Pursuant to Section 242 and 245 of the
                General Corporation Law of the State of Delaware
 
                        --------------------------------
 
         The undersigned, for the purpose of amending and restating the
Certificate of Incorporation of NitroMed, Inc., as amended and supplemented
heretofore under the laws of the State of Delaware, hereby certifies as follows:
 
         1. The original name of this corporation is NitroMed, Inc. and the
original Certificate of Incorporation was filed with the Secretary of State of
the State of Delaware on March 9, 1992. A Restated Certificate of Incorporation
was filed on December 2, 1993. A Certificate of Amendment was filed on each of
July 27, 1994 and December 20, 1994. A Second Restated Certificate of
Incorporation was filed on June 19, 1995. A Certificate of Amendment was filed
on each of January 10, 1996, April 11, 1996, September 30, 1996, December 17,
1996, February 10, 1997, April 4, 1997, April 7, 1997 and July 31, 1997. A Third
Restated Certificate of Incorporation was filed on December 31, 1997. A Fourth
Restated Certificate of Incorporation was filed on May 17, 1999. A Certificate
of Amendment was filed on May 1, 2000. A Fifth Restated Certificate of
Incorporation was filed on May 22, 2001. A Certificate of Amendment was filed on
June 15, 2001. A Sixth Restated Certificate of Incorporation was filed on
November 20, 2001. A Certificate of Amendment was filed on each of May 12, 2003,
July 31, 2003 and [_____], 2003.
 
         2. At a meeting of the Board of Directors of the Corporation a
resolution was duly adopted pursuant to Sections 242 and 245 of the General
Corporation Law of the State of Delaware, setting forth this Restated
Certificate of Incorporation and declaring said Restated Certificate to be
advisable. The stockholders of the Corporation duly approved and adopted said
proposed Restated Certificate of Incorporation by written consent in accordance
with Sections 228, 242 and 245 of the General Corporation Law of State of
Delaware, and written notice of such consent has been given to all stockholders
who have not consented in writing to said Restated Certificate of Incorporation.
 
 
        3. The Certificate of Incorporation of this Corporation, as previously
amended, is hereby further amended and restated in its entirety to read as
follows:
 
        FIRST:   The name of the Corporation is Nitromed, Inc.
 
        SECOND: The address of the Corporation's registered office in the
State of Delaware is Corporation Trust Center, 1209 Orange Street, in the
City of Wilmington, County of New Castle. The name of its registered agent at
such address is The Corporation Trust Company.
 
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        THIRD: The nature of the business or purposes to be conducted or
promoted by the Corporation is to engage in any lawful act or activity for
which corporations may be organized under the General Corporation Law of
Delaware.
 
        FOURTH: The total number of shares of all classes of stock which the
Corporation shall have authority to issue is 70,000,000 shares, consisting of
(i) 65,000,000 shares of Common Stock, $0.01 par value per share ("Common
Stock"), and (ii) 5,000,000 shares of Preferred Stock, $0.01 par value per
share ("Preferred Stock").
 
        The following is a statement of the designations and the powers,
privileges and rights, and the qualifications, limitations or restrictions
thereof in respect of each class of capital stock of the Corporation.
 
A        COMMON STOCK.
 
 
        1.  GENERAL.  The voting,  dividend and  liquidation  rights of the
holders of the Common Stock are subject to and qualified by the rights of the
holders of the  Preferred  Stock of any series as may be designated by the
Board of Directors upon any issuance of the Preferred Stock of any series.
 
        2.  VOTING.  The holders of the Common Stock shall have voting
rights at all meetings of  stockholders,  each such holder being  entitled to
one vote for each share  thereof held by such holder.  There shall be no
cumulative voting.
 
        The number of authorized shares of Common 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 stock of the
Corporation entitled to vote, irrespective of the provisions of Section
242(b)(2) of the General Corporation Law of Delaware.
 
        3.  DIVIDENDS.  Dividends  may be  declared  and  paid on the  Common
 Stock  from  funds  lawfully  available therefor  as and when  determined
by the Board of  Directors  and  subject to any  preferential  dividend or
other rights of any then outstanding Preferred Stock.
 
        4.  LIQUIDATION.  Upon the dissolution or liquidation of the
Corporation,  whether  voluntary or involuntary, holders of Common Stock will
be entitled to receive all assets of the  Corporation  available for
distribution  to its stockholders, subject to any preferential or other
rights of any then outstanding Preferred Stock.
 
B        PREFERRED STOCK.
 
         Preferred Stock may be issued from time to time in one or more series,
each of such series to have such terms as stated or expressed herein and in the
resolution or resolutions providing for the issue of such series adopted by the
Board of Directors of the Corporation as hereinafter provided. Any shares of
Preferred Stock which may be redeemed, purchased or acquired by the Corporation
may be reissued except as otherwise provided by law. Different series of
Preferred Stock shall not be construed to constitute different classes of shares
for the purposes of voting by classes unless expressly provided.
 
         Authority is hereby expressly granted to the Board of Directors from
time to time to issue the Preferred Stock in one or more series, and in
connection with the creation of any such series, by resolution or resolutions
providing for the issuance of the shares thereof, to determine and fix the
number of shares of such series and such voting powers, full or limited, or no
voting powers, and such designations, preferences and relative participating,
optional or other special rights, and qualifications,
 
 
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limitations or restrictions thereof, including without limitation thereof,
dividend rights, conversion rights, redemption privileges and liquidation
preferences, as shall be stated and expressed in such resolutions, all to the
full extent now or hereafter permitted by the General Corporation Law of
Delaware. Without limiting the generality of the foregoing, the resolutions
providing for issuance of any series of Preferred Stock may provide that such
series shall be superior or rank equally or be junior to the Preferred Stock
of any other series to the extent permitted by law. Except as otherwise
provided in this Certificate of Incorporation, no vote of the holders of the
Preferred Stock or Common Stock shall be a prerequisite to the designation or
issuance of any shares of any series of the Preferred Stock authorized by and
complying with the conditions of this Certificate of Incorporation, the right
to have such vote being expressly waived by all present and future holders of
the capital stock of the Corporation.
 
         The number of authorized shares of Preferred Stock may be increased
or decreased (but not below the number of shares then outstanding) by the
affirmative vote of the holders of a majority of the stock of the Corporation
entitled to vote, irrespective of the provisions of Section 242(b)(2) of the
General Corporation Law of Delaware.
 
         FIFTH: Except as otherwise provided herein, the Corporation reserves
the right to amend, alter, change or repeal any provision contained in this
Certificate of Incorporation, in the manner now or hereafter prescribed by
statute and this Certificate of Incorporation, and all rights conferred upon
stockholders herein are granted subject to this reservation.
 
         SIXTH: In furtherance and not in limitation of the powers conferred
upon it by the laws of the State of Delaware, the Board of Directors shall
have the power to adopt, amend, alter or repeal the Corporation's By-laws.
The affirmative vote of a majority of the directors present at any regular or
special meeting of the Board of Directors at which a quorum is present shall
be required to adopt, amend, alter or repeal the Corporation's By-laws. The
Corporation's By-laws also may be adopted, amended, altered or repealed by
the affirmative vote of the holders of at least seventy-five percent (75%) of
the votes which all the stockholders would be entitled to cast in any annual
election of directors or class of directors. Notwithstanding any other
provisions of law, this Certificate of Incorporation or the By-Laws of the
Corporation, and notwithstanding the fact that a lesser percentage may be
specified by law, the affirmative vote of the holders of at least
seventy-five percent (75%) of the votes which all the stockholders would be
entitled to cast in any annual election of directors or class of directors
shall be required to amend or repeal, or to adopt any provision inconsistent
with, this Article SIXTH.
 
        SEVENTH: Except to the extent that the General Corporation Law of
Delaware prohibits the elimination or limitation of liability of directors
for breaches of fiduciary duty, no director of the Corporation shall be
personally liable to the Corporation or its stockholders for monetary damages
for any breach of fiduciary duty as a director, notwithstanding any provision
of law imposing such liability. No amendment to or repeal of this provision
shall apply to or have any effect on the liability or alleged liability of
any director of the Corporation for or with respect to any acts or omissions
of such director occurring prior to such amendment or repeal.
 
        EIGHTH:  The Corporation shall provide indemnification as follows:
 
        1.  ACTIONS, SUITS AND PROCEEDINGS OTHER THAN BY OR IN THE RIGHT OF
THE CORPORATION. The Corporation shall indemnify each person who was or is a
party or threatened to be made a party to any threatened, pending or
completed action, suit or proceeding, whether civil, criminal, administrative
or investigative (other than an action by or in the right of the Corporation)
by reason of the fact that he or she is or was, or has agreed to become, a
director or officer of the Corporation, or is or was serving, or has agreed
to serve, at the request of the Corporation, as a director, officer, partner,
employee or trustee of, or in a similar capacity with, another corporation,
partnership, joint venture, trust or other enterprise
 
 
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(including any employee benefit plan) (all such persons being referred to
hereafter as an "Indemnitee"), or by reason of any action alleged to have
been taken or omitted in such capacity, against all expenses (including
attorneys' fees), judgments, fines and amounts paid in settlement actually
and reasonably incurred by or on behalf of Indemnitee in connection with such
action, suit or proceeding and any appeal therefrom, if Indemnitee acted in
good faith and in a manner which Indemnitee reasonably believed to be in, or
not opposed to, the best interests of the Corporation, and, with respect to
any criminal action or proceeding, had no reasonable cause to believe his or
her conduct was unlawful. The termination of any action, suit or proceeding
by judgment, order, settlement, conviction or upon a plea of NOLO CONTENDERE
or its equivalent, shall not, of itself, create a presumption that Indemnitee
did not act in good faith and in a manner which Indemnitee reasonably
believed to be in, or not opposed to, the best interests of the Corporation,
and, with respect to any criminal action or proceeding, had reasonable cause
to believe that his or her conduct was unlawful.
 
       2. ACTIONS OR SUITS BY OR IN THE RIGHT OF THE CORPORATION. The
Corporation shall indemnify any Indemnitee who was or is a party to or
threatened to be made a party to any threatened, pending or completed action
or suit by or in the right of the Corporation to procure a judgment in its
favor by reason of the fact that Indemnitee is or was, or has agreed to
become, a director or officer of the Corporation, or is or was serving, or
has agreed to serve, at the request of the Corporation, as a director,
officer, partner, employee or trustee of, or in a similar capacity with,
another corporation, partnership, joint venture, trust or other enterprise
(including any employee benefit plan), or by reason of any action alleged to
have been taken or omitted in such capacity, against all expenses (including
attorneys' fees) and, to the extent permitted by law, amounts paid in
settlement actually and reasonably incurred by or on behalf of Indemnitee in
connection with such action, suit or proceeding and any appeal therefrom, if
Indemnitee acted in good faith and in a manner which Indemnitee reasonably
believed to be in, or not opposed to, the best interests of the Corporation,
except that no indemnification shall be made under this Section 2 in respect
of any claim, issue or matter as to which Indemnitee shall have been adjudged
to be liable to the Corporation, unless, and only to the extent, that the
Court of Chancery of Delaware shall determine upon application that, despite
the adjudication of such liability but in view of all the circumstances of
the case, Indemnitee is fairly and reasonably entitled to indemnity for such
expenses (including attorneys' fees) which the Court of Chancery of Delaware
shall deem proper.
 
       3. INDEMNIFICATION FOR EXPENSES OF SUCCESSFUL PARTY. Notwithstanding
any other provisions of this Article, to the extent that an Indemnitee has
been successful, on the merits or otherwise, in defense of any action, suit
or proceeding referred to in Sections 1 and 2 of this Article EIGHTH, or in
defense of any claim, issue or matter therein, or on appeal from any such
action, suit or proceeding, Indemnitee shall be indemnified against all
expenses (including attorneys' fees) actually and reasonably incurred by or
on behalf of Indemnitee in connection therewith. Without limiting the
foregoing, if any action, suit or proceeding is disposed of, on the merits or
otherwise (including a disposition without prejudice), without (i) the
disposition being adverse to Indemnitee, (ii) an adjudication that Indemnitee
was liable to the Corporation, (iii) a plea of guilty or NOLO CONTENDERE by
Indemnitee, (iv) an adjudication that Indemnitee did not act in good faith
and in a manner he reasonably believed to be in or not opposed to the best
interests of the Corporation, and (v) with respect to any criminal
proceeding, an adjudication that Indemnitee had reasonable cause to believe
his conduct was unlawful, Indemnitee shall be considered for the purposes
hereof to have been wholly successful with respect thereto.
 
       4. NOTIFICATION AND DEFENSE OF CLAIM. As a condition precedent to an
Indemnitee's right to be indemnified, such Indemnitee must notify the
Corporation in writing as soon as practicable of any action, suit, proceeding
or investigation involving such Indemnitee for which indemnity will or could
be sought. With respect to any action, suit, proceeding or investigation of
which the Corporation is so notified, the Corporation will be entitled to
participate therein at its own expense and/or to assume the defense thereof
at its own expense, with legal counsel reasonably acceptable to Indemnitee.
After notice
 
 
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from the Corporation to Indemnitee of its election so to assume such defense,
the Corporation shall not be liable to Indemnitee for any legal or other
expenses subsequently incurred by Indemnitee in connection with such action,
suit, proceeding or investigation, other than as provided below in this
Section 4. Indemnitee shall have the right to employ his or her own counsel
in connection with such action, suit, proceeding or investigation, but the
fees and expenses of such counsel incurred after notice from the Corporation
of its assumption of the defense thereof shall be at the expense of
Indemnitee unless (i) the employment of counsel by Indemnitee has been
authorized by the Corporation, (ii) counsel to Indemnitee shall have
reasonably concluded that there may be a conflict of interest or position on
any significant issue between the Corporation and Indemnitee in the conduct
of the defense of such action, suit, proceeding or investigation or (iii) the
Corporation shall not in fact have employed counsel to assume the defense of
such action, suit, proceeding or investigation, in each of which cases the
fees and expenses of counsel for Indemnitee shall be at the expense of the
Corporation, except as otherwise expressly provided by this Article. The
Corporation shall not be entitled, without the consent of Indemnitee, to
assume the defense of any claim brought by or in the right of the Corporation
or as to which counsel for Indemnitee shall have reasonably made the
conclusion provided for in clause (ii) above. The Corporation shall not be
required to indemnify Indemnitee under this Article EIGHTH for any amounts
paid in settlement of any action, suit, proceeding or investigation effected
without its written consent. The Corporation shall not settle any action,
suit, proceeding or investigation in any manner which would impose any
penalty or limitation on Indemnitee without Indemnitee's written consent.
Neither the Corporation nor Indemnitee will unreasonably withhold or delay
its consent to any proposed settlement.
 
       5.   ADVANCE OF EXPENSES. Subject to the provisions of Section 6 of
this Article EIGHTH, in the event that the Corporation does not assume the
defense pursuant to Section 4 of this Article EIGHTH of any action, suit,
proceeding or investigation of which the Corporation receives notice under
this Article, any expenses (including attorneys' fees) incurred by or on
behalf of Indemnitee in defending an action, suit, proceeding or
investigation or any appeal therefrom shall be paid by the Corporation in
advance of the final disposition of such matter; PROVIDED, however, that the
payment of such expenses incurred by or on behalf of Indemnitee in advance of
the final disposition of such matter shall be made only upon receipt of an
undertaking by or on behalf of Indemnitee to repay all amounts so advanced in
the event that it shall ultimately be determined that Indemnitee is not
entitled to be indemnified by the Corporation as authorized in this Article;
and further provided that no such advancement of expenses shall be made under
this Article EIGHTH if it is determined (in the manner described in Section
6) that (i) Indemnitee did not act in good faith and in a manner he
reasonably believed to be in, or not opposed to, the best interests of the
Corporation, or (ii) with respect to any criminal action or proceeding,
Indemnitee had reasonable cause to believe his conduct was unlawful. Such
undertaking shall be accepted without reference to the financial ability of
Indemnitee to make such repayment.
 
       6.   PROCEDURE FOR INDEMNIFICATION. In order to obtain indemnification
or advancement of expenses pursuant to Section 1, 2, 3 or 5 of this Article
EIGHTH, an Indemnitee shall submit to the Corporation a written request. Any
such advancement of expenses shall be made promptly, and in any event within
30 days after receipt by the Corporation of the written request of
Indemnitee, unless the Corporation determines within such 30-day period that
Indemnitee did not meet the applicable standard of conduct set forth in
Section 1, 2 or 5 of this Article EIGHTH, as the case may be. Any such
indemnification, unless ordered by a court, shall be made with respect to
requests under Section 1 or 2 only as authorized in the specific case upon a
determination by the Corporation that the indemnification of Indemnitee is
proper because Indemnitee has met the applicable standard of conduct set
forth in Section 1 or 2, as the case may be. Such determination shall be made
in each instance (a) by a majority vote of the directors of the Corporation
consisting of persons who are not at that time parties to the action, suit or
proceeding in question ("disinterested directors"), whether or not a quorum,
(b) by a committee of disinterested directors designated by majority vote of
disinterested directors, whether or not a quorum, (c) if there are no
disinterested directors, or if the disinterested directors so direct, be
independent legal
 
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counsel (who may, to the extent permitted by law, by regular legal counsel to
the Corporation) in a written opinion, or (d) by the stockholders of the
Corporation.
 
       7.  REMEDIES. The right to indemnification or advancement of expenses
as granted by this Article shall be enforceable by Indemnitee in any court of
competent jurisdiction. Neither the failure of the Corporation to have made a
determination prior to the commencement of such action that indemnification
is proper in the circumstances because Indemnitee has met the applicable
standard of conduct, nor an actual determination by the Corporation pursuant
to Section 6 of this Article EIGHTH that Indemnitee has not met such
applicable standard of conduct, shall be a defense to the action or create a
presumption that Indemnitee has not met the applicable standard of conduct.
Indemnitee's expenses (including attorneys' fees) reasonably incurred in
connection with successfully establishing Indemnitee's right to
indemnification, in whole or in part, in any such proceeding shall also be
indemnified by the Corporation.
 
       8.   LIMITATIONS. Notwithstanding anything to the contrary in this
Article, except as set forth in Section 7 of the Article EIGHTH, the
Corporation shall not indemnify an Indemnitee pursuant to this Article EIGHTH
in connection with a proceeding (or part thereof) initiated by such
Indemnitee unless the initiation thereof was approved by the Board of
Directors of the Corporation. Notwithstanding anything to the contrary in
this Article, the Corporation shall not indemnify an Indemnitee to the extent
such Indemnitee is reimbursed from the proceeds of insurance, and in the
event the Corporation makes any indemnification payments to an Indemnitee and
such Indemnitee is subsequently reimbursed from the proceeds of insurance,
such Indemnitee shall promptly refund indemnification payments to the
Corporation to the extent of such insurance reimbursement.
 
       9.   SUBSEQUENT AMENDMENT. No amendment, termination or repeal of this
Article or of the relevant provisions of the General Corporation Law of
Delaware or any other applicable laws shall affect or diminish in any way the
rights of any Indemnitee to indemnification under the provisions hereof with
respect to any action, suit, proceeding or investigation arising out of or
relating to any actions, transactions or facts occurring prior to the final
adoption of such amendment, termination or repeal.
 
       10.  OTHER RIGHTS. The indemnification and advancement of expenses
provided by this Article shall not be deemed exclusive of any other rights to
which an Indemnitee seeking indemnification or advancement of expenses may be
entitled under any law (common or statutory), agreement or vote of
stockholders or disinterested directors or otherwise, both as to action in
Indemnitee's official capacity and as to action in any other capacity while
holding office for the Corporation, and shall continue as to an Indemnitee
who has ceased to be a director or officer, and shall inure to the benefit of
the estate, heirs, executors and administrators of Indemnitee. Nothing
contained in this Article shall be deemed to prohibit, and the Corporation is
specifically authorized to enter into, agreements with officers and directors
providing indemnification rights and procedures different from those set
forth in this Article. In addition, the Corporation may, to the extent
authorized from time to time by its Board of Directors, grant indemnification
rights to other employees or agents of the Corporation or other persons
serving the Corporation and such rights may be equivalent to, or greater or
less than, those set forth in this Article.
 
       11.  PARTIAL INDEMNIFICATION. If an Indemnitee is entitled under any
provision of this Article to indemnification by the Corporation for some or a
portion of the expenses (including attorneys' fees), judgments, fines or
amounts paid in settlement actually and reasonably incurred by or on behalf
of Indemnitee in connection with any action, suit, proceeding or
investigation and any appeal therefrom but not, however, for the total amount
thereof, the Corporation shall nevertheless indemnify Indemnitee for the
portion of such expenses (including attorneys' fees), judgments, fines or
amounts paid in settlement to which Indemnitee is entitled.
 
 
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       12.  INSURANCE. The Corporation may purchase and 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 (including any employee benefit plan) against any
expense, liability or loss incurred by him in any such capacity, or arising
out of his status as such, whether or not the Corporation would have the
power to indemnify such person against such expense, liability or loss under
the General Corporation Law of Delaware.
 
       13.  SAVINGS CLAUSE. If this Article or any portion hereof shall be
invalidated on any ground by any court of competent jurisdiction, then the
Corporation shall nevertheless indemnify each Indemnitee as to any expenses
(including attorneys' fees), judgments, fines and amounts paid in settlement
in connection with any action, suit, proceeding or investigation, whether
civil, criminal or administrative, including an action by or in the right of
the Corporation, to the fullest extent permitted by any applicable portion of
this Article that shall not have been invalidated and to the fullest extent
permitted by applicable law.
 
       14.  DEFINITIONS.  Terms used herein and defined in Section 145(h) and
Section 145(i) of the General Corporation Law of Delaware shall have the
respective meanings assigned to such terms in such Section 145(h) and Section
145(i).
 
       NINTH:  This Article is inserted for the  management of the business
and for the conduct of the affairs of the Corporation.
 
       1.  NUMBER OF DIRECTORS; ELECTION OF DIRECTORS. Subject to the rights
of holders of any series of Preferred Stock to elect directors, the number of
directors of the Corporation shall not be less than three. The exact number
of directors within the limitations specified in the preceding sentence shall
be determined from time to time by, or in the manner provided in, the By-laws
of the Corporation. Election of directors need not be by written ballot,
except as and to the extent provided in the By-laws of the Corporation.
 
       2.   TENURE. Subject to the rights of holders of any series of
Preferred Stock to elect directors, each director shall hold office until the
next annual meeting of stockholders and until a successor is elected and
qualified, or until such director's earlier death, resignation or removal.
 
       3.   QUORUM. A majority of the directors at any time in office shall
constitute a quorum for the transaction of business. In the event one or more
of the directors shall be disqualified to vote at any meeting, then the
required quorum shall be reduced by one for each director so disqualified. In
no case, however, shall less than one-third of the number of directors fixed
pursuant to Section 1 of this Article NINTH constitute a quorum. If at any
meeting of the Board of Directors there shall be less than such a quorum, a
majority of the directors present may adjourn the meeting from time to time
without further notice other than announcement at the meeting, until a quorum
shall be present.
 
       4.   ACTION AT MEETING. Every act or decision done or made by a
majority of the directors present at a meeting duly held at which a quorum is
present shall be regarded as the act of the Board of Directors unless a
greater number is required by law, by this Certificate of Incorporation, or
by the By-laws of the Corporation.
 
       5.   REMOVAL. Subject to the rights of holders of any series of
Preferred Stock, directors of the Corporation may be removed only for cause
by the affirmative vote of the holders of at least seventy-five percent (75%)
of the votes which all the stockholders would be entitled to cast in any
annual election of directors or class of directors.
 
 
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       6.  VACANCIES. Subject to the rights of holders of any series of
Preferred Stock, any vacancy or newly created directorships in the Board of
Directors, however occurring, shall be filled only by vote of a majority of
the directors then in office, although less than a quorum, or by a sole
remaining director and shall not be filled by the stockholders. A director
elected to fill a vacancy shall be elected to hold office until the next
annual meeting of stockholders, subject to the election and qualification of
his successor and to his earlier death, resignation or removal.
 
       7.  STOCKHOLDER NOMINATIONS AND INTRODUCTION OF BUSINESS, ETC. Advance
notice of stockholder nominations for election of directors and other
business to be brought by stockholders  before a meeting of stockholders
shall be given in the manner provided by the By-laws of the Corporation.
 
       8.  AMENDMENTS TO ARTICLE. Notwithstanding any other provisions of
law, this Certificate of Incorporation or the By-laws of the Corporation, and
notwithstanding the fact that a lesser percentage may be specified by law,
the affirmative vote of the holders of at least seventy-five percent (75%) of
the votes which all the stockholders would be entitled to cast in any annual
election of directors or class of directors shall be required to amend or
repeal, or to adopt any provision inconsistent with, this Article NINTH.
 
       TENTH: Stockholders of the Corporation may not take any action by
written consent in lieu of a meeting. Notwithstanding any other provisions of
law, this Certificate of Incorporation or the By-laws of the Corporation, and
notwithstanding the fact that a lesser percentage may be specified by law,
the affirmative vote of the holders of at least seventy-five percent (75%) of
the votes which all the stockholders would be entitled to cast in any annual
election of directors or class of directors shall be required to amend or
repeal, or to adopt any provision inconsistent with, this Article TENTH.
 
       ELEVENTH: Special meetings of stockholders for any purpose or purposes
may be called at any time by the Board of Directors, the Chairman of the
Board or the Chief Executive Officer, but such special meetings may not be
called by any other person or persons. Business transacted at any special
meeting of stockholders shall be limited to matters relating to the purpose
or purposes stated in the notice of meeting. Notwithstanding any other
provision of law, this Certificate of Incorporation or the By-laws of the
Corporation, and notwithstanding the fact that a lesser percentage may be
specified by law, the affirmative vote of the holders of at least
seventy-five percent (75%) of the votes which all the stockholders would be
entitled to cast in any annual election of directors or class of directors
shall be required to amend or repeal, or to adopt any provision inconsistent
with, this Article ELEVENTH.
 
       IN WITNESS WHEREOF, the Corporation has caused this Restated
Certificate of Incorporation, which restates, integrates and amends the
Certificate of Incorporation of the Corporation, has been executed by its
duly authorized officer this ____ day of ___________, 2003.
 
 
 
 
                                  NITROMED, INC.
 
 
                                  By:
                                     ----------------------------------------
                                     Name:     Michael D. Loberg
                                     Title:    Chief Executive Officer
 
 
 
 
                            CERTIFICATE OF AMENDMENT
                                       OF
                   SIXTH RESTATED CERTIFICATE OF INCORPORATION
                                       OF
                                 NITROMED, INC.
 
                         Pursuant to Section 242 of the
                General Corporation Law of the State of Delaware
 
                            ------------------------
 
     NitroMed, Inc. (hereinafter called the "Corporation"), organized and
existing under and by virtue of the General Corporation Laws of the State of
Delaware, does hereby certify as follows:
 
     At a meeting of the Board of Directors of the Corporation a resolution was
duly adopted, pursuant to Section 242 of the General Corporation Law of the
State of Delaware, setting forth amendments to the Sixth Restated Certificate of
Incorporation of the Corporation and declaring said amendments to be advisable.
The stockholders of the Corporation duly adopted said amendments by written
consent in accordance with Sections 228 and 242 of the General Corporation Law
of the State of Delaware. Said amendments have been duly adopted in accordance
with Section 242 of the General Corporation Law of the State of Delaware. The
resolution setting forth the amendments is as follows:
 
     RESOLVED: That the Sixth Restated Certificate of Incorporation of the
Corporation (the "Restated Certificate") be amended as follows:
 
     (1)  Article III(a) of the Restated Certificate is deleted in its entirety
          and the following new paragraph is inserted in lieu thereof:
 
               "(a) AUTHORIZATION. The total number of shares of all classes of
          stock which the Corporation shall have authority to issue is
          69,688,320 consisting of:
 
                    (i) 34,688,320 shares of Preferred Stock, par value $.01 per
          share (the "Preferred Stock"), of which:
 
                         (A) 5,000,000 shares shall be designated "Series A
          Convertible Preferred Stock" (the "Series A Stock");
 
                         (B) 17,005,330 shares shall be designated "Series B
          Convertible Preferred Stock" (the "Series B Stock");
 
                         (C) 3,157,895 shares shall have been designated "Series
          C Convertible Preferred Stock" (the "Series C Stock");
 
                         (D) 2,137,791 shares shall have been designated "Series
          D Convertible Preferred Stock" (the "Series D Stock");
 
                         (E) 7,137,304 shares shall have been designated "Series
          E Convertible Preferred Stock" (the "Series E Stock");
 
                         (F) 250,000 shares shall have been designated "Series F
          Junior Convertible Preferred Stock" (the "Series F Junior Stock"); and
 
 
<Page>
 
 
                    (ii) 35,000,000 shares of Common Stock, par value $.01 per
          share (the "Common Stock")."
 
     (2)  Article III, Section A.7, of the Restated Certificate shall be amended
          by adding the following new Section A.7(k):
 
               "A.7(k) All holders of record of shares of Series Preferred Stock
          shall be given written notice of the mandatory conversion of Series
          Preferred Stock pursuant to Section A.7(j) above and such notice shall
          designate the place for such mandatory conversion. Such notice need
          not be given in advance of the mandatory conversion date. Such notice
          shall be sent by first class or registered mail, postage prepaid, or
          given by electronic communication in compliance with the provisions of
          the General Corporation Law, to each record holder of Series Preferred
          Stock. Upon receipt of such notice, each holder of shares of Series
          Preferred Stock shall surrender his or its certificate or certificates
          for all such shares to the Corporation at the place designated in such
          notice, and shall thereafter receive certificates for the number of
          shares of Common Stock to which such holder is entitled pursuant to
          Section A.7(j) above. As of the conversion date of the Series
          Preferred Stock, all outstanding shares of Series Preferred Stock
          shall be deemed to have been converted into shares of Common Stock,
          which shall be deemed to be outstanding of record, and all rights with
          respect to the Series Preferred Stock so converted, including the
          rights, if any, to receive notices and vote (other than as a holder of
          Common Stock), will terminate, except only the rights of the holders
          thereof, upon surrender of their certificate or certificates therefor,
          to receive certificates for the number of shares of Common Stock into
          which such Series Preferred Stock has been converted. All certificates
          evidencing shares of Series Preferred Stock converted into shares of
          Common Stock pursuant to Section A.7(j) above shall, from and after
          such conversion date, be deemed to have been retired and canceled,
          notwithstanding the failure of the holder or holders thereof to
          surrender such certificates to the Corporation in accordance with the
          provisions hereof. Upon the closing of the sale of shares of Common
          Stock in a firm commitment underwriting meeting the requirements of
          Section A.7(j) above, the number of authorized shares of Series A
          Stock, Series B Stock, Series C Stock, Series D Stock, Series E Stock
          and Series F Junior Stock shall be automatically reduced by the number
          of shares of Series A Stock, Series B Stock, Series C Stock, Series D
          Stock, Series E Stock and Series F Junior Stock that had been
          designated as Series A Stock, Series B Stock, Series C Stock, Series D
          Stock, Series E Stock and Series F Junior Stock and all provisions
          included under Article III(a)(i)(A)-(F) and all references to the
          Series A Stock, Series B Stock, Series C Stock, Series D Stock, Series
          E Stock and Series F Junior Stock in this Sixth Restated Certificate
          of Incorporation shall be deleted and of no further force or effect.
 
     (3)  Article X of the Restated Certificate is deleted in its entirely and
          the following is inserted in lieu thereof:
 
                                   "ARTICLE X
 
                             LIMITATION OF LIABILITY
 
               Except to the extent that the General Corporation Law of Delaware
          prohibits the elimination or limitation of liability of directors for
          breaches of fiduciary duty, no director of the Corporation shall be
          personally liable to the Corporation or its stockholders for monetary
          damages for any breach of fiduciary duty as a director,
          notwithstanding any provision of law imposing such liability. No
          amendment to or repeal of this provision shall apply to or have any
          effect on the liability or alleged liability
 
 
                                      -2-
 
<Page>
 
 
          of any director of the Corporation for or with respect to any acts or
          omissions of such director occurring prior to such amendment or
          repeal."
 
     (4)  Article XI of the Restated Certificate is deleted in its entirely and
          the following is inserted in lieu thereof:
 
                                   "ARTICLE XI
 
                                 INDEMNIFICATION
 
          The Corporation shall provide indemnification as follows:
 
               1. ACTIONS, SUITS AND PROCEEDINGS OTHER THAN BY OR IN THE RIGHT
          OF THE CORPORATION. The Corporation shall indemnify each person who
          was or is a party or threatened to be made a party to any threatened,
          pending or completed action, suit or proceeding, whether civil,
          criminal, administrative or investigative (other than an action by or
          in the right of the Corporation) by reason of the fact that he or she
          is or was, or has agreed to become, a director or officer of the
          Corporation, or is or was serving, or has agreed to serve, at the
          request of the Corporation, as a director, officer, partner, employee
          or trustee of, or in a similar capacity with, another corporation,
          partnership, joint venture, trust or other enterprise (including any
          employee benefit plan) (all such persons being referred to hereafter
          as an "Indemnitee"), or by reason of any action alleged to have been
          taken or omitted in such capacity, against all expenses (including
          attorneys' fees), judgments, fines and amounts paid in settlement
          actually and reasonably incurred by or on behalf of Indemnitee in
          connection with such action, suit or proceeding and any appeal
          therefrom, if Indemnitee acted in good faith and in a manner which
          Indemnitee reasonably believed to be in, or not opposed to, the best
          interests of the Corporation, and, with respect to any criminal action
          or proceeding, had no reasonable cause to believe his or her conduct
          was unlawful. The termination of any action, suit or proceeding by
          judgment, order, settlement, conviction or upon a plea of nolo
          contendere or its equivalent, shall not, of itself, create a
          presumption that Indemnitee did not act in good faith and in a manner
          which Indemnitee reasonably believed to be in, or not opposed to, the
          best interests of the Corporation, and, with respect to any criminal
          action or proceeding, had reasonable cause to believe that his or her
          conduct was unlawful.
 
               2. ACTIONS OR SUITS BY OR IN THE RIGHT OF THE CORPORATION. The
          Corporation shall indemnify any Indemnitee who was or is a party to or
          threatened to be made a party to any threatened, pending or completed
          action or suit by or in the right of the Corporation to procure a
          judgment in its favor by reason of the fact that Indemnitee is or was,
          or has agreed to become, a director or officer of the Corporation, or
          is or was serving, or has agreed to serve, at the request of the
          Corporation, as a director, officer, partner, employee or trustee of,
          or in a similar capacity with, another corporation, partnership, joint
          venture, trust or other enterprise (including any employee benefit
          plan), or by reason of any action alleged to have been taken or
          omitted in such capacity, against all expenses (including attorneys'
          fees) and, to the extent permitted by law, amounts paid in settlement
          actually and reasonably incurred by or on behalf of Indemnitee in
          connection with such action, suit or proceeding and any appeal
          therefrom, if Indemnitee acted in good faith and in a manner which
          Indemnitee reasonably believed to be in, or not opposed to, the best
          interests of the Corporation, except that no indemnification shall be
          made under this Section 2 in respect of any claim, issue or matter as
          to which Indemnitee shall have been adjudged to be liable to the
          Corporation, unless, and only to the extent, that the Court of
          Chancery of Delaware shall determine upon application that, despite
          the adjudication of such liability but in view of all the
          circumstances of the case,
 
 
                                      -3-
 
 
<Page>
 
 
          Indemnitee is fairly and reasonably entitled to indemnity for such
          expenses (including attorneys' fees) which the Court of Chancery of
          Delaware shall deem proper.
 
               3. INDEMNIFICATION FOR EXPENSES OF SUCCESSFUL PARTY.
          Notwithstanding any other provisions of this Article XI, to the extent
          that an Indemnitee has been successful, on the merits or otherwise, in
          defense of any action, suit or proceeding referred to in Sections 1
          and 2 of this Article XI, or in defense of any claim, issue or matter
          therein, or on appeal from any such action, suit or proceeding,
          Indemnitee shall be indemnified against all expenses (including
          attorneys' fees) actually and reasonably incurred by or on behalf of
          Indemnitee in connection therewith. Without limiting the foregoing, if
          any action, suit or proceeding is disposed of, on the merits or
          otherwise (including a disposition without prejudice), without (i) the
          disposition being adverse to Indemnitee, (ii) an adjudication that
          Indemnitee was liable to the Corporation, (iii) a plea of guilty or
          nolo contendere by Indemnitee, (iv) an adjudication that Indemnitee
          did not act in good faith and in a manner he reasonably believed to be
          in or not opposed to the best interests of the Corporation, and (v)
          with respect to any criminal proceeding, an adjudication that
          Indemnitee had reasonable cause to believe his conduct was unlawful,
          Indemnitee shall be considered for the purposes hereof to have been
          wholly successful with respect thereto.
 
               4. NOTIFICATION AND DEFENSE OF CLAIM. As a condition precedent to
          an Indemnitee's right to be indemnified, such Indemnitee must notify
          the Corporation in writing as soon as practicable of any action, suit,
          proceeding or investigation involving such Indemnitee for which
          indemnity will or could be sought. With respect to any action, suit,
          proceeding or investigation of which the Corporation is so notified,
          the Corporation will be entitled to participate therein at its own
          expense and/or to assume the defense thereof at its own expense, with
          legal counsel reasonably acceptable to Indemnitee. After notice from
          the Corporation to Indemnitee of its election so to assume such
          defense, the Corporation shall not be liable to Indemnitee for any
          legal or other expenses subsequently incurred by Indemnitee in
          connection with such action, suit, proceeding or investigation, other
          than as provided below in this Section 4. Indemnitee shall have the
          right to employ his or her own counsel in connection with such action,
          suit, proceeding or investigation, but the fees and expenses of such
          counsel incurred after notice from the Corporation of its assumption
          of the defense thereof shall be at the expense of Indemnitee unless
          (i) the employment of counsel by Indemnitee has been authorized by the
          Corporation, (ii) counsel to Indemnitee shall have reasonably
          concluded that there may be a conflict of interest or position on any
          significant issue between the Corporation and Indemnitee in the
          conduct of the defense of such action, suit, proceeding or
          investigation or (iii) the Corporation shall not in fact have employed
          counsel to assume the defense of such action, suit, proceeding or
          investigation, in each of which cases the fees and expenses of counsel
          for Indemnitee shall be at the expense of the Corporation, except as
          otherwise expressly provided by this Article XI. The Corporation shall
          not be entitled, without the consent of Indemnitee, to assume the
          defense of any claim brought by or in the right of the Corporation or
          as to which counsel for Indemnitee shall have reasonably made the
          conclusion provided for in clause (ii) above. The Corporation shall
          not be required to indemnify Indemnitee under this Article XI for any
          amounts paid in settlement of any action, suit, proceeding or
          investigation effected without its written consent. The Corporation
          shall not settle any action, suit, proceeding or investigation in any
          manner which would impose any penalty or limitation on Indemnitee
          without Indemnitee's written consent. Neither the Corporation nor
          Indemnitee will unreasonably withhold or delay its consent to any
          proposed settlement.
 
 
                                      -4-
 
 
<Page>
 
 
               5. ADVANCE OF EXPENSES. Subject to the provisions of Section 6 of
          this Article XI, in the event that the Corporation does not assume the
          defense pursuant to Section 4 of this Article XI of any action, suit,
          proceeding or investigation of which the Corporation receives notice
          under this Article XI, any expenses (including attorneys' fees)
          incurred by or on behalf of Indemnitee in defending an action, suit,
          proceeding or investigation or any appeal therefrom shall be paid by
          the Corporation in advance of the final disposition of such matter;
          provided, however, that the payment of such expenses incurred by or on
          behalf of Indemnitee in advance of the final disposition of such
          matter shall be made only upon receipt of an undertaking by or on
          behalf of Indemnitee to repay all amounts so advanced in the event
          that it shall ultimately be determined that Indemnitee is not entitled
          to be indemnified by the Corporation as authorized in this Article XI;
          and further provided that no such advancement of expenses shall be
          made under this Article XI if it is determined (in the manner
          described in Section 6) that (i) Indemnitee did not act in good faith
          and in a manner he reasonably believed to be in, or not opposed to,
          the best interests of the Corporation, or (ii) with respect to any
          criminal action or proceeding, Indemnitee had reasonable cause to
          believe his conduct was unlawful. Such undertaking shall be accepted
          without reference to the financial ability of Indemnitee to make such
          repayment.
 
               6. PROCEDURE FOR INDEMNIFICATION. In order to obtain
          indemnification or advancement of expenses pursuant to Section 1, 2, 3
          or 5 of this Article XI, an Indemnitee shall submit to the Corporation
          a written request. Any such advancement of expenses shall be made
          promptly, and in any event within 30 days after receipt by the
          Corporation of the written request of Indemnitee, unless the
          Corporation determines within such 30-day period that Indemnitee did
          not meet the applicable standard of conduct set forth in Section 1, 2
          or 5 of this Article XI, as the case may be. Any such indemnification,
          unless ordered by a court, shall be made with respect to requests
          under Section 1 or 2 only as authorized in the specific case upon a
          determination by the Corporation that the indemnification of
          Indemnitee is proper because Indemnitee has met the applicable
          standard of conduct set forth in Section 1 or 2, as the case may be.
          Such determination shall be made in each instance (a) by a majority
          vote of the directors of the Corporation consisting of persons who are
          not at that time parties to the action, suit or proceeding in question
          ("disinterested directors"), whether or not a quorum, (b) by a
          committee of disinterested directors designated by majority vote of
          disinterested directors, whether or not a quorum, (c) if there are no
          disinterested directors, or if the disinterested directors so direct,
          be independent legal counsel (who may, to the extent permitted by law,
          by regular legal counsel to the Corporation) in a written opinion, or
          (d) by the stockholders of the Corporation.
 
               7. REMEDIES. The right to indemnification or advancement of
          expenses as granted by this Article XI shall be enforceable by
          Indemnitee in any court of competent jurisdiction. Neither the failure
          of the Corporation to have made a determination prior to the
          commencement of such action that indemnification is proper in the
          circumstances because Indemnitee has met the applicable standard of
          conduct, nor an actual determination by the Corporation pursuant to
          Section 6 of this Article XI that Indemnitee has not met such
          applicable standard of conduct, shall be a defense to the action or
          create a presumption that Indemnitee has not met the applicable
          standard of conduct. Indemnitee's expenses (including attorneys' fees)
          reasonably incurred in connection with successfully establishing
          Indemnitee's right to indemnification, in whole or in part, in any
          such proceeding shall also be indemnified by the Corporation.
 
               8. LIMITATIONS. Notwithstanding anything to the contrary in this
          Article XI, except as set forth in Section 7 of the Article XI, the
          Corporation shall not indemnify an
 
 
                                      -5-
 
 
<Page>
 
 
          Indemnitee pursuant to this Article XI in connection with a proceeding
          (or part thereof) initiated by such Indemnitee unless the initiation
          thereof was approved by the Board of Directors of the Corporation.
          Notwithstanding anything to the contrary in this Article XI, the
          Corporation shall not indemnify an Indemnitee to the extent such
          Indemnitee is reimbursed from the proceeds of insurance, and in the
          event the Corporation makes any indemnification payments to an
          Indemnitee and such Indemnitee is subsequently reimbursed from the
          proceeds of insurance, such Indemnitee shall promptly refund
          indemnification payments to the Corporation to the extent of such
          insurance reimbursement.
 
               9. SUBSEQUENT AMENDMENT. No amendment, termination or repeal of
          this Article XI or of the relevant provisions of the General
          Corporation Law of Delaware or any other applicable laws shall affect
          or diminish in any way the rights of any Indemnitee to indemnification
          under the provisions hereof with respect to any action, suit,
          proceeding or investigation arising out of or relating to any actions,
          transactions or facts occurring prior to the final adoption of such
          amendment, termination or repeal.
 
               10. OTHER RIGHTS. The indemnification and advancement of expenses
          provided by this Article XI shall not be deemed exclusive of any other
          rights to which an Indemnitee seeking indemnification or advancement
          of expenses may be entitled under any law (common or statutory),
          agreement or vote of stockholders or disinterested directors or
          otherwise, both as to action in Indemnitee's official capacity and as
          to action in any other capacity while holding office for the
          Corporation, and shall continue as to an Indemnitee who has ceased to
          be a director or officer, and shall inure to the benefit of the
          estate, heirs, executors and administrators of Indemnitee. Nothing
          contained in this Article XI shall be deemed to prohibit, and the
          Corporation is specifically authorized to enter into, agreements with
          officers and directors providing indemnification rights and procedures
          different from those set forth in this Article XI. In addition, the
          Corporation may, to the extent authorized from time to time by its
          Board of Directors, grant indemnification rights to other employees or
          agents of the Corporation or other persons serving the Corporation and
          such rights may be equivalent to, or greater or less than, those set
          forth in this Article XI.
 
               11. PARTIAL INDEMNIFICATION. If an Indemnitee is entitled under
          any provision of this Article to indemnification by the Corporation
          for some or a portion of the expenses (including attorneys' fees),
          judgments, fines or amounts paid in settlement actually and reasonably
          incurred by or on behalf of Indemnitee in connection with any action,
          suit, proceeding or investigation and any appeal therefrom but not,
          however, for the total amount thereof, the Corporation shall
          nevertheless indemnify Indemnitee for the portion of such expenses
          (including attorneys' fees), judgments, fines or amounts paid in
          settlement to which Indemnitee is entitled.
 
               12. INSURANCE. The Corporation may purchase and 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 (including any
          employee benefit plan) against any expense, liability or loss incurred
          by him in any such capacity, or arising out of his status as such,
          whether or not the Corporation would have the power to indemnify such
          person against such expense, liability or loss under the General
          Corporation Law of Delaware.
 
               13. SAVINGS CLAUSE. If this Article or any portion hereof shall
          be invalidated on any ground by any court of competent jurisdiction,
          then the Corporation shall nevertheless indemnify each Indemnitee as
          to any expenses (including attorneys'
 
 
                                      -6-
 
 
<Page>
 
 
          fees), judgments, fines and amounts paid in settlement in connection
          with any action, suit, proceeding or investigation, whether civil,
          criminal or administrative, including an action by or in the right of
          the Corporation, to the fullest extent permitted by any applicable
          portion of this Article that shall not have been invalidated and to
          the fullest extent permitted by applicable law.
 
               14. DEFINITIONS. Terms used herein and defined in Section 145(h)
          and Section 145(i) of the General Corporation Law of Delaware shall
          have the respective meanings assigned to such terms in such Section
          145(h) and Section 145(i)."
 
     (5)  A new Article XII shall be inserted into the Restated Certificate as
          follows:
 
                                  "ARTICLE XII
 
                              STOCKHOLDER MEETINGS
 
          Upon the closing of the sale of shares of Common Stock in a firm
          commitment underwriting meeting the requirements of Section A.7(j),
          Stockholders of the Corporation may not take any action by written
          consent in lieu of a meeting. Notwithstanding any other provisions of
          law, this Sixth Restated Certificate of Incorporation or the By-laws
          of the Corporation, and notwithstanding the fact that a lesser
          percentage may be specified by law, the affirmative vote of the
          holders of at least seventy-five percent (75%) of the votes which all
          the stockholders would be entitled to cast in any annual election of
          directors or class of directors shall be required to amend or repeal,
          or to adopt any provision inconsistent with, this Article XII."
 
     IN WITNESS WHEREOF, the Corporation has caused this Certificate of
Amendment to be signed by its President and Chief Executive Officer on this ___
day of _________, 2003.
 
 
                             NITROMED, INC.
 
 
                             By:
                                ---------------------------------------------
                                Name:  Michael D. Loberg
                                Title: President and Chief Executive Officer