<PAGE>

                                                                     EXHIBIT 4.6

                                SIPEX CORPORATION

                       STAND-ALONE STOCK OPTION AGREEMENT

NOTICE OF STOCK OPTION GRANT

      [NAME]

      [ADDRESS]

      _______________

                  You have been granted a Nonstatutory Stock Option to purchase
      Common Stock of the Company, subject to the terms and conditions of this
      Agreement, as follows:

      Date of Grant                     _________________________

      Vesting Commencement Date         _________________________

      Exercise Price per Share         $_________________________

      Total Number of Shares Granted    _________________________

      Total Exercise Price             $_________________________

      Term/Expiration Date:             _________________________

      Vesting Schedule:

      This Option shall vest and may be exercised, in whole or in part, in
accordance with the following schedule, subject to the Optionee continuing to be
a Service Provider on such dates:

<TABLE>
<S>                                               <C>
Prior to<<VestDate1>>                             <<SHARES6>>shares

As of<<VestDate1>>but prior to<<VestDate2>>       <<SHARES2>>shares

As of<<VestDate2>>but prior to<<VestDate3>>       an additional<<SHARES3>>shares

As of<<VestDate3>>but prior to<<VestDate4>>       an additional<<SHARES4>>shares
</TABLE>

<PAGE>

<TABLE>
<S>                                               <C>
As of<<VestDate4>>but prior to<<VestDate5>>       an additional<<SHARES5>>shares

As of<<VestDate5>>                                an additional<<SHARES5>>shares
</TABLE>

            Termination Period

                  This Option may be exercised for three (3) months after
      Optionee ceases to be a Service Provider in accordance with Section 7 of
      this Agreement. Upon the death or Disability of the Optionee, this Option
      may be exercised for one hundred and eighty (180) days after the Optionee
      ceases to be a Service Provider in accordance with Sections 8 and 9 of
      this Agreement. In no event shall this Option be exercised later that the
      Term/Expiration Date provided. [THIS OPTION SHALL TERMINATE AND
      IMMEDIATELY CEASE TO BE EXERCISABLE ON THE DATE OPTIONEE RECEIVES NOTICE
      OF TERMINATION FOR CAUSE IN ACCORDANCE WITH SECTION 10 OF THIS AGREEMENT.]

AGREEMENT

      Definitions. As used herein, the following definitions shall apply:

            "Agreement" means this stock option agreement between the Company
and Optionee evidencing the terms and conditions of this Option.

            "Applicable Laws" means the requirements relating to the
administration of stock options under U.S. state corporate laws, U.S. federal
and state securities laws, the Code, any stock exchange or quotation system on
which the Common Stock is listed or quoted and the applicable laws of any
foreign country or jurisdiction that may apply to this Option.

            "Board" means the Board of Directors of the Company or any committee
of the Board that has been designated by the Board to administer this Agreement.

            ["CAUSE" MEANS CONDUCT INVOLVING ONE OR MORE OF THE FOLLOWING: (I)
THE SUBSTANTIAL AND CONTINUING FAILURE OF THE OPTIONEE, AFTER NOTICE THEREOF, TO
RENDER SERVICES TO THE COMPANY OR ANY PARENT OR SUBSIDIARY IN ACCORDANCE WITH
THE TERMS OR REQUIREMENTS OF OPTIONEE'S EMPLOYMENT OR BUSINESS RELATIONSHIP;
(II) GROSS NEGLIGENCE, WILLFUL MISCONDUCT, DISHONESTY, FRAUD OR BREACH OF
FIDUCIARY DUTY TO THE COMPANY OR ANY PARENT OR SUBSIDIARY; (III) THE COMMISSION
OF AN ACT OF EMBEZZLEMENT OR FRAUD; (IV) DELIBERATE DISREGARD OF THE RULES OR
POLICIES OF THE COMPANY OR ANY PARENT OR SUBSIDIARY, OR BREACH OF AN EMPLOYMENT
OR OTHER AGREEMENT WITH THE COMPANY OR ANY PARENT OR SUBSIDIARY, EITHER OF WHICH
RESULTS IN SIGNIFICANT DIRECT OR INDIRECT LOSS, DAMAGE OR INJURY TO THE COMPANY
OR ANY PARENT OR SUBSIDIARY; (V) THE UNAUTHORIZED DISCLOSURE OF ANY TRADE SECRET
OR CONFIDENTIAL INFORMATION OF THE COMPANY OR ANY PARENT OR SUBSIDIARY; OR (VI)
THE COMMISSION OF AN ACT WHICH CONSTITUTES UNFAIR COMPETITION WITH THE COMPANY
OR ANY PARENT OR SUBSIDIARY OR WHICH INDUCES ANY CUSTOMER OR SUPPLIER TO BREACH
A CONTRACT WITH THE COMPANY OR ANY PARENT OR SUBSIDIARY.]

            "Code" means the Internal Revenue Code of 1986, as amended.

            "Common Stock" means the common stock of the Company.

                                      -2-
<PAGE>

            "Company" means SIPEX Corporation, a Massachusetts corporation.

            "Consultant" means any person, including an advisor, engaged by the
Company or a Parent or Subsidiary to render services to such entity.

            "Director" means a member of the Board.

            "Disability" means total and permanent disability as defined in
Section 22(e)(3) of the Code.

            "Employee" means any person, including Officers and Directors,
employed by the Company or any Parent or Subsidiary of the Company. A Service
Provider shall not cease to be an Employee in the case of (i) any leave of
absence approved by the Company or (ii) transfers between locations of the
Company or between the Company, its Parent, any Subsidiary, or any successor.
Neither service as a Director nor payment of a director's fee by the Company
shall be sufficient to constitute "employment" by the Company.

            "Exchange Act" means the Securities Exchange Act of 1934, as
amended.

            "Fair Market Value" means, as of any date, the value of Common Stock
determined as follows:

                        If the Common Stock is listed on any established stock
exchange or a national market system, including without limitation the Nasdaq
National Market or The Nasdaq SmallCap Market of The Nasdaq Stock Market, its
Fair Market Value shall be the closing sales price for such stock (or the
closing bid, if no sales were reported) as quoted on such exchange or system for
the last market trading day prior to the time of determination, as reported in
The Wall Street Journal or such other source as the Administrator deems
reliable;

                        If the Common Stock is regularly quoted by a recognized
securities dealer but selling prices are not reported, its Fair Market Value
shall be the mean between the high bid and low asked prices for the Common Stock
on the last market trading day prior to the day of determination; or

                        In the absence of an established market for the Common
Stock, the Fair Market Value thereof shall be determined in good faith by the
Board.

            "Nonstatutory Stock Option" means an Option not intended to qualify
as an incentive stock option within the meaning of Section 422 of the Code and
the regulations promulgated thereunder.

            "Notice of Grant" means a written notice, in Part I of this
Agreement, evidencing certain the terms and conditions of this Option grant. The
Notice of Grant is part of the Option Agreement.

            "Officer" means a person who is an officer of the Company within the
meaning of Section 16 of the Exchange Act and the rules and regulations
promulgated thereunder.

            "Option" means this stock option.

            "Optioned Stock" means the Common Stock subject to this Option.

            "Optionee" means the person named in the Notice of Grant or such
person's successor.

            "Parent" means a "parent corporation," whether now or hereafter
existing, as defined in Section 424(e) of the Code.

                                      -3-
<PAGE>

            "Service Provider" means an Employee, Director or Consultant.

            "Share" means a share of the Common Stock, as adjusted in accordance
with Section 11 [CHANGE TO SECTION 10 IF THE TERMINATION FOR CAUSE SECTION IS
REMOVED] of this Agreement.

            "Subsidiary" means a "subsidiary corporation", whether now or
hereafter existing, as defined in Section 424(f) of the Code.

      Grant of Option. The Board hereby grants to the Optionee named in the
Notice of Grant attached as Part I of this Agreement the Option to purchase the
number of Shares, as set forth in the Notice of Grant, at the exercise price per
share set forth in the Notice of Grant (the "Exercise Price"), subject to the
terms and conditions of this Agreement.

      Exercise of Option.

            Right to Exercise. This Option is exercisable during its term in
accordance with the Vesting Schedule set out in the Notice of Grant and the
applicable provisions of this Agreement.

            Method of Exercise. This Option is exercisable by delivery of an
exercise notice, in the form attached as Exhibit A (the "Exercise Notice"),
which shall state the election to exercise the Option, the number of Shares in
respect of which the Option is being exercised (the "Exercised Shares"), and
such other representations and agreements as may be required by the Company. The
Exercise Notice shall be completed by the Optionee and delivered to Secretary of
the Company. The Exercise Notice shall be accompanied by payment of the
aggregate Exercise Price as to all Exercised Shares. This Option shall be deemed
to be exercised upon receipt by the Company of such fully executed Exercise
Notice accompanied by such aggregate Exercise Price.

            Legal Compliance. No Shares shall be issued pursuant to the exercise
of this Option unless such issuance and exercise complies with Applicable Laws.
Assuming such compliance, for income tax purposes the Exercised Shares shall be
considered transferred to the Optionee on the date the Option is exercised with
respect to such Exercised Shares.

            Buyout Provisions. The Board may at any time offer to buy out for a
payment in cash or Shares an Option previously granted based on such terms and
conditions as the Board shall establish and communicate to the Optionee at the
time that such offer is made.

      Method of Payment. Payment of the aggregate Exercise Price shall be by any
of the following, or a combination thereof, at the election of the Optionee:

            cash or check;

            [CONSIDERATION RECEIVED BY THE COMPANY UNDER A CASHLESS EXERCISE
PROGRAM IMPLEMENTED BY THE COMPANY;] or [TO BE REMOVED FOR GRANTS TO OFFICERS]

            surrender of other Shares which (i) in the case of Shares acquired
upon exercise of an option, have been owned by the Optionee for more than six
(6) months on the date of surrender, AND (ii) have a Fair Market Value on the
date of surrender equal to the aggregate Exercise Price of the Exercised Shares.

      Non-Transferability of Option. This Option may not be transferred in any
manner otherwise than by will or by the laws of descent or distribution and may
be exercised during the lifetime of Optionee only by the

                                      -4-
<PAGE>

Optionee. The terms of this Agreement shall be binding upon the executors,
administrators, heirs, successors and assigns of the Optionee.

      Term of Option. This Option may be exercised only within the term set out
in the Notice of Grant, and may be exercised during such term only in accordance
with the terms of this Agreement.

      Termination of Relationship as a Service Provider. If the Optionee ceases
to be a Service Provider (other than for death or Disability), this Option may
be exercised for a period of three (3) months after the date of such termination
(but in no event later than the expiration date of this Option as set forth in
the Notice of Grant) to the extent that the Option is vested on the date of such
termination. To the extent that the Optionee does not exercise this Option
within the time specified herein, the Option shall terminate.

      Disability of Optionee. If the Optionee ceases to be a Service Provider as
a result of the Optionee's Disability, this Option may be exercised for a period
of one hundred and eighty (180) days after the date of such termination (but in
no event later than the expiration date of this Option as set forth in the
Notice of Grant) to the extent that the Option is vested on the date of such
termination. To the extent that Optionee does not exercise this Option within
the time specified herein, the Option shall terminate.

      Death of Optionee. If the Optionee dies while a Service Provider, the
Option may be exercised at any time within one hundred and eighty (180) days
following the date of death (but in no event later than the expiration date of
this Option as set forth in the Notice of Grant), by the Optionee's estate or by
a person who acquired the right to exercise the Option by bequest or
inheritance, but only to the extent that the Optionee was entitled to exercise
the Option at the date of death. If, after death, the Optionee's estate or a
person who acquired the right to exercise the Option by bequest or inheritance
does not exercise the Option within the time specified herein, the Option shall
terminate.

      [TERMINATION FOR CAUSE. IF THE OPTIONEE IS TERMINATED FOR CAUSE, THIS
OPTION SHALL TERMINATE IMMEDIATELY UPON THE OPTIONEE'S RECEIPT OF WRITTEN NOTICE
OF SUCH TERMINATION AND SHALL THEREAFTER NOT BE EXERCISABLE TO ANY EXTENT
WHATSOEVER.]

      Adjustments upon Changes in Capitalization, Dissolution, Merger or Asset
Sale. Subject to any required action by the stockholders of the Company, the
number of shares of Common Stock and class of securities covered by this Option,
as well as the price per share of Common Stock covered by this Option and the
vesting schedule, shall be proportionately adjusted (or a substituted option may
be granted) for any increase or decrease in the number of issued shares of
Common Stock resulting from a stock split, reverse stock split, stock dividend,
extraordinary cash dividend, recapitalization, reorganization, merger,
consolidation, combination, exchange of shares, liquidation, spin-off, split-up
or other similar event or reclassification of the Common Stock, or any other
increase or decrease in the number of issued shares of Common Stock effected
without receipt of consideration by the Company; provided, however, that
conversion of any convertible securities of the Company shall not be deemed to
have been "effected without receipt of consideration." Such adjustment shall be
made by the Board, whose determination in that respect shall be final, binding
and conclusive. Except as expressly provided herein, no issuance by the Company
of shares of stock of any class, or securities convertible into shares of stock
of any class, shall affect, and no adjustment by reason thereof shall be made
with respect to, the number or price of shares of Common Stock subject to this
Option.

      Notices. Any notice to be given to the Company hereunder shall be in
writing and shall be addressed to the Company at its then current principal
executive office or to such other address as the Company may hereafter designate
to the Optionee by notice as provided in this Section. Any notice to be given to
the Optionee hereunder shall be addressed to the Optionee at the address set
forth beneath his signature hereto, or

                                      -5-
<PAGE>

at such other address as the Optionee may hereafter designate to the Company by
notice as provided herein. A notice shall be deemed to have been duly given when
personally delivered or mailed by registered or certified mail to the party
entitled to receive it.

      Tax Consequences. Some of the federal tax consequences relating to this
Option, as of the date of this Option, are set forth below. THIS SUMMARY IS
NECESSARILY INCOMPLETE, AND THE TAX LAWS AND REGULATIONS ARE SUBJECT TO CHANGE.
THE OPTIONEE SHOULD CONSULT A TAX ADVISER BEFORE EXERCISING THIS OPTION OR
DISPOSING OF THE SHARES.

            Exercising the Option. The Optionee may incur regular federal income
tax liability upon exercise of a Nonstatutory Stock Option (an "NSO"). The
Optionee will be treated as having received compensation income (taxable at
ordinary income tax rates) equal to the excess, if any, of the Fair Market Value
of the Exercised Shares on the date of exercise over their aggregate Exercise
Price. If the Optionee is an Employee or a former Employee, the Company will be
required to withhold from his or her compensation or collect from Optionee and
pay to the applicable taxing authorities an amount in cash equal to a percentage
of this compensation income at the time of exercise, and may refuse to honor the
exercise and refuse to deliver Shares if such withholding amounts are not
delivered at the time of exercise.

            Disposition of Shares. If the Optionee holds NSO Shares for at least
one year, any gain realized on disposition of the Shares will be treated as
long-term capital gain for federal income tax purposes.

      Entire Agreement; Governing Law. This Agreement constitute the entire
agreement of the parties with respect to the subject matter hereof and supersede
in their entirety all prior undertakings and agreements of the Company and
Optionee with respect to the subject matter hereof, and may not be modified
adversely to the Optionee's interest except by means of a writing signed by the
Company and Optionee. This agreement is governed by the internal substantive
laws, but not the choice of law rules, of Massachusetts.

      NO GUARANTEE OF CONTINUED SERVICE. OPTIONEE ACKNOWLEDGES AND AGREES THAT
THE VESTING OF SHARES PURSUANT TO THE VESTING SCHEDULE HEREOF IS EARNED ONLY BY
CONTINUING AS A SERVICE PROVIDER AT THE WILL OF THE COMPANY (AND NOT THROUGH THE
ACT OF BEING HIRED, BEING GRANTED AN OPTION OR PURCHASING SHARES HEREUNDER).
OPTIONEE FURTHER ACKNOWLEDGES AND AGREES THAT THIS AGREEMENT, THE TRANSACTIONS
CONTEMPLATED HEREUNDER AND THE VESTING SCHEDULE SET FORTH HEREIN DO NOT
CONSTITUTE AN EXPRESS OR IMPLIED PROMISE OF CONTINUES ENGAGEMENT AS A SERVICE
PROVIDER FOR THE VESTING PERIOD, FOR ANY PERIOD, OR AT ALL, AND SHALL NOT
INTERFERE WITH OPTIONEE'S RIGHT OR THE COMPANY'S RIGHT TO TERMINATE OPTIONEE'S
RELATIONSHIP AS A SERVICE PROVIDER AT ANY TIME, WITH OR WITHOUT CAUSE.

                                      -6-
<PAGE>

      By your signature and the signature of the Company's representative below,
you and the Company agree that this Option is granted under and governed by the
terms and conditions of this Agreement. Optionee has reviewed this Agreement in
its entirety, has had an opportunity to obtain the advice of counsel prior to
executing this Agreement and fully understands all provisions of this Agreement.
Optionee hereby agrees to accept as binding, conclusive and final all decisions
or interpretations of the Board upon any questions relating to this Agreement.
Optionee further agrees to notify the Company upon any change in the residence
address indicated below.

OPTIONEE                                   SIPEX CORPORATION

_____________________________________      _____________________________________
Signature                                  By

_____________________________________      _____________________________________
Print Name                                 Title

_____________________________________      _____________________________________
Residence Address

_____________________________________

_____________________________________

                                      -7-
<PAGE>

                                    EXHIBIT A

                                SIPEX CORPORATION

                                 EXERCISE NOTICE

SIPEX Corporation
22 Linnell Circle, Billerica
Massachusetts 01821

Attention:

      17.   Exercise of Option. Effective as of today, ________________, 200_,
the undersigned ("Purchaser") hereby elects to purchase ______________ shares
(the "Shares") of the Common Stock of SIPEX Corporation (the "Company") under
and pursuant to the Stock Option Agreement dated [_____________] (the "Option
Agreement"). The purchase price for the Shares shall be [$_______], as required
by the Option Agreement.

      18.   Delivery of Payment. Purchaser herewith delivers to the Company the
full purchase price for the Shares.

      19.   Representations of Purchaser. Purchaser acknowledges that Purchaser
has received, read and understood the Option Agreement and agrees to abide by
and be bound by their terms and conditions.

      20.   Rights as Shareholder. Until the issuance (as evidenced by the
appropriate entry on the books of the Company or of a duly authorized transfer
agent of the Company) of the Shares, no right to vote or receive dividends or
any other rights as a stockholder shall exist with respect to the Optioned
Stock, notwithstanding the exercise of the Option. The Shares so acquired shall
be issued to the Optionee as soon as practicable after exercise of the Option.
No adjustment will be made for a dividend or other right for which the record
date is prior to the date of issuance, except as provided in Section 11 [CHANGE
TO SECTION 10 IF THE TERMINATION FOR CAUSE SECTION IS REMOVED] of the Option
Agreement.

      21.   Tax Consultation. Purchaser understands that Purchaser may suffer
adverse tax consequences as a result of Purchaser's purchase or disposition of
the Shares. Purchaser represents that Purchaser has consulted with any tax
consultants Purchaser deems advisable in connection with the purchase or
disposition of the Shares and that Purchaser is not relying on the Company for
any tax advice.

      22.   Successors and Assigns. The Company may assign any of its rights
under this Exercise Notice to single or multiple assignees, and this Exercise
Notice shall inure to the benefit of the successors and assigns of the Company.
Subject to the restrictions on transfer herein set forth, this Exercise Notice
shall be binding upon Optionee and his or her heirs, executors, administrators,
successors and assigns.

      23.   Interpretation. Any dispute regarding the interpretation of this
Exercise Notice shall be submitted by Optionee or by the Company forthwith to
the Administrator which shall review such dispute at

<PAGE>

its next regular meeting. The resolution of such a dispute by the Administrator
shall be final and binding on all parties.

      24.   Entire Agreement; Governing Law. The Option Agreement is
incorporated herein by reference. This Agreement, and the Option Agreement
constitute the entire agreement of the parties with respect to the subject
matter hereof and supersede in their entirety all prior undertakings and
agreements of the Company and Purchaser with respect to the subject matter
hereof, and may not be modified adversely to the Purchaser's interest except by
means of a writing signed by the Company and Purchaser. This agreement is
governed by the internal substantive laws, but not the choice of law rules, of
Massachusetts.

Submitted by:                              Accepted by:

OPTIONEE                                   SIPEX CORPORATION

_____________________________________      _____________________________________
Signature

_____________________________________      _____________________________________
Print Name

_____________________________________      _____________________________________
Address:                                   Address:

_____________________________________      22 Linnell Circle, Billerica

_____________________________________      Massachusetts 01821

                                           Date Received: _________________

                                      -2-