<PAGE>   1
                                                                     Exhibit 4.6

                                SIPEX CORPORATION

                             STOCK OPTION AGREEMENT

           SIPEX Corporation (the "Company") hereby grants the following option
to purchase Common Stock, $.01 par value per share (the "Common Stock"), of the
Company pursuant to an action of the Board of Directors (the "Board") of the
Company on January 16, 2001. The terms and conditions attached hereto are also a
part hereof.

<TABLE>
<S>                                                                              <C>
         Name of employee (the "Employee" or "Optionee"):                        Bruce Diamond

         Date of this option grant:                                              January 16, 2001

         Number of shares of the Company's Common Stock subject to this option
         ("Option Shares"):                                                      500,000

         Option exercise price per share:                                        $12.688

         Number of Option Shares subject to vesting schedule:                    500,000

         Vesting Start Date:                                                     January 2, 2002

         Vesting Schedule. If the Employee has continued to be employed by the
         Company or any Related Corporation (as defined in Section 2 hereof) on
         the following dates, the Employee may exercise this option for the
         number of shares of Common Stock as set forth below.

         Prior to January 2, 2002                                                0 shares

         As of January 2, 2002 but prior to January 2, 2003                      100,000 shares

         As of January 2, 2003 but prior to January 2, 2004                      an additional 100,000 shares

         As of January 2, 2004 but prior to January 2, 2005                      an additional 100,000 shares

         As of January 2, 2005 but prior to January 2, 2006                      an additional 100,000 shares

         As of January 2, 2006 but prior to January 2, 2007                      an additional 100,000 shares


         Payment alternatives:                                                   Section 6(a) (i) through (iv)
</TABLE>

                                        SIPEX CORPORATION


___________________________________
Signature of Optionee


___________________________________
Street Address


___________________________________     By: __________________________
City/State/Zip Code                         James E. Donegan
                                            Chairman and Chief Executive Officer
<PAGE>   2
SIPEX CORPORATION

STOCK OPTION AGREEMENT -- INCORPORATED TERMS AND CONDITIONS


           1. GRANT AS NON-QUALIFIED STOCK OPTION. This option is a
non-statutory stock option and is not intended to qualify as an incentive stock
option under Section 422 of the Internal Revenue Code of 1986, as amended, and
the regulations thereunder (the "Code").

           2. VESTING OF OPTION IF EMPLOYMENT CONTINUES. The Employee may
exercise this option for the number of shares of Common Stock set forth on the
vesting schedule on the cover page hereof if the Employee has continued to be
employed by the Company or any present or future parent or subsidiary of the
Company (collectively, "Related Corporations") in accordance with such vesting
schedule. Notwithstanding the foregoing, the Board may, in its discretion,
accelerate the date that any installment of this option becomes exercisable. The
foregoing rights are cumulative and (subject to Sections 3 or 4 hereof if the
Employee ceases to be employed by the Company) may be exercised only before the
date which is ten years from the date of this option grant.

           3. TERMINATION OF EMPLOYMENT.

                (a) TERMINATION OTHER THAN FOR CAUSE. If the Employee ceases to
be employed by the Company and all Related Corporations, other than by reason of
death or disability as defined in Section 4 or termination for Cause as defined
in the Employment Agreement between the Employee and the Company dated
__________ ___, 2001 (the "Employment Agreement"), no further installments of
this option shall become exercisable, and this option shall terminate (and may
no longer be exercised) after the passage of three months from the Employee's
last day of employment, but in no event later than the scheduled expiration
date. In such a case, the Employee's only rights hereunder shall be those which
are properly exercised before the termination of this option.

                (b) TERMINATION FOR CAUSE. If the employment of the Employee is
terminated for Cause, this option shall terminate upon the Employee's receipt of
written notice of such termination and shall thereafter not be exercisable to
any extent whatsoever.

           4. DEATH; DISABILITY.

                (a) DEATH. If the Employee dies while in the employ of the
Company or any Related Corporation, this option may be exercised, to the extent
otherwise exercisable on the date of his or her death, by the Employee's estate,
personal representative or beneficiary to whom this option has been assigned
pursuant to Section 9, at any time within 180 days after the date of death, but
not later than the scheduled expiration date.

                (b) DISABILITY. If the Employee ceases to be employed by the
Company and all Related Corporations by reason of his disability, this option
may be exercised, to the extent otherwise exercisable on the date of the
termination of his employment, at any time within 180 days after such
termination, but not later than the scheduled expiration date. The term
disability shall have the meaning ascribed in Section 3(D) of the Employment
Agreement.

                (c) EFFECT OF TERMINATION. At the expiration of the 180-day
period provided in paragraph (a) or (b) of this Section 4 or the scheduled
expiration date, whichever is the earlier, this option shall terminate (and
shall no longer be exercisable) and the only rights hereunder shall be those as
to which the option was properly exercised before such termination.

           5. PARTIAL EXERCISE. This option may be exercised in part at any time
and from time to time within the above limits, except that this option may not
be exercised for a fraction of a share.

           6. PAYMENT OF ALTERNATIVES. (a) The exercise price shall be paid in
the following manner:
<PAGE>   3
                      (i)        in cash or by check;

                      (ii)       subject to paragraph 6(b) below, by delivery of
                                 shares of the Company's Common Stock having a
                                 fair market value equal, as of the date of
                                 exercise, to the option exercise price;

                      (iii)      by delivery of an assignment satisfactory in
                                 form and substance to the Company of a
                                 sufficient amount of the proceeds from the sale
                                 of the Option Shares and an instruction to the
                                 broker or selling agent to pay that amount to
                                 the Company; or

                      (v)        by any combination of the foregoing.

                     In the case of (ii) above, fair market value as of the date
           of exercise shall be determined as of the last business day for which
           such prices or quotes are available prior to the date of exercise and
           shall mean (i) the average (on that date) of the high and low prices
           of the Common Stock on the principal national securities exchange on
           which the Common Stock is traded, if the Common Stock is then traded
           on a national securities exchange; or (ii) the last reported sale
           price (on that date) of the Common Stock on the Nasdaq National
           Market, if the Common Stock is not then traded on a national
           securities exchange; or (iii) the closing bid price (or average of
           bid prices) last quoted (on that date) by an established quotation
           service for over-the-counter securities, if the Common Stock is not
           reported on the Nasdaq National Market. If the Common Stock is not
           publicly traded at the time of exercise, "fair market value" shall
           mean the fair value of the Common Stock as determined by the Board
           after taking into consideration all factors which it deems
           appropriate, including, without limitation, recent sale and offer
           prices of the Common Stock in private transactions negotiated at
           arm's length.

                (b) LIMITATIONS ON PAYMENT BY DELIVERY OF COMMON STOCK. If the
Employee delivers Common Stock held by the Employee ("Old Stock") to the Company
in full or partial payment of the option price, and the Old Stock so delivered
is subject to restrictions or limitations imposed by agreement between the
Employee and the Company, an equivalent number of Option Shares shall be subject
to all restrictions and limitations applicable to the Old Stock to the extent
that the Employee paid for the Option Shares by delivery of Old Stock, in
addition to any restrictions or limitations imposed by this Agreement.
Notwithstanding the foregoing, the Employee may not pay any part of the exercise
price hereof by transferring Common Stock to the Company unless such Common
Stock has been owned by the Employee free of any substantial risk of forfeiture
for at least six months.

           7. METHOD OF EXERCISING OPTION. Subject to the terms and conditions
of this Agreement, this option may be exercised by written notice to the Company
at its principal executive office, or to such transfer agent as the Company
shall designate. Such notice shall state the election to exercise this option
and the number of Option Shares for which it is being exercised and shall be
signed by the person or persons so exercising this option. Such notice shall be
accompanied by payment of the full purchase price of such shares, and the
Company shall deliver a certificate or certificates representing such shares as
soon as practicable after the notice shall be received. Such certificate or
certificates shall be registered in the name of the person or persons so
exercising this option (or, if this option shall be exercised by the Employee
and if the Employee shall so request in the notice exercising this option, shall
be registered in the name of the Employee and another person jointly, with right
of survivorship). In the event this option shall be exercised, pursuant to
Section 4 hereof, by any person or persons other than the Employee, such notice
shall be accompanied by appropriate proof of the right of such person or persons
to exercise this option.

           8. SECURITIES LAWS RESTRICTIONS ON RESALE. Until registered under the
Securities Act of 1933, as amended, or any successor statute (the "Securities
Act"), the Option Shares will be of an illiquid nature and will be deemed to be
"restricted securities" for purposes of the Securities Act. Accordingly, such
shares must be sold in compliance with the registration requirements of the
Securities Act or an exemption therefrom. Unless the Option Shares have been
registered under the Securities Act, each certificate evidencing any of the
Option Shares shall bear a legend substantially as follows:
<PAGE>   4
           "The shares represented by this certificate are subject to
           restrictions on transfer and may not be sold, exchanged, transferred,
           pledged, hypothecated or otherwise disposed of except in accordance
           with and subject to all the terms and conditions of a certain Stock
           Option Agreement dated as of January 16, 2001, a copy of which the
           Company will furnish to the holder of this certificate upon request
           and without charge."

           9. OPTION NOT TRANSFERABLE. This option is not transferable or
assignable except by will or by the laws of descent and distribution. During the
Optionee's lifetime only the Optionee can exercise this option.

           10. NO OBLIGATION TO EXERCISE OPTION. The grant and acceptance of
this option imposes no obligation on the Optionee to exercise it.

           11. ADJUSTMENTS. In the event of any stock split, stock dividend,
extraordinary cash dividend, recapitalization, reorganization, merger,
consolidation, combination, exchange of shares, liquidation, spin-off, split-up,
or other similar change in capitalization or event, the number and class of
securities, vesting schedule and exercise price per share of this option shall
be adjusted by the Company (or a substituted option may be granted) to the
extent the Board shall determine, in good faith, that such an adjustment (or
substitution) is appropriate. If Section 13 hereof applies for any event, this
Section 11 shall not be applicable. Except as is expressly provided in this
Section 11, no adjustment shall be made for dividends or similar rights for
which the record date is prior to such date of exercise.

           12. WITHHOLDING TAXES. If the Company or any Related Corporation in
its discretion determines that it is obligated to withhold any tax in connection
with the exercise of this option, or in connection with the transfer of, or the
lapse of restrictions on, any Common Stock or other property acquired pursuant
to this option, the Optionee hereby agrees that the Company or any Related
Corporation may withhold from the Optionee's wages or any other remuneration the
appropriate amount of tax. At the discretion of the Company or Related
Corporation, the amount required to be withheld may be withheld in cash from
such wages or other remuneration or in kind from the Common Stock or other
property otherwise deliverable to the Optionee on exercise of this option. The
Optionee further agrees that, if the Company or Related Corporation does not
withhold an amount from the Optionee's wages or other remuneration sufficient to
satisfy the withholding obligation of the Company or Related Corporation, the
Optionee will make reimbursement on demand, in cash, for the amount
underwithheld.

           13. ACQUISITION OF THE COMPANY.

                      (a) CONSEQUENCES OF AN ACQUISITION. In the event of an
Acquisition, and (i) the successor (a "Successor To The Business") fails to
assume the obligations of the Company under this Agreement or (ii) Employee's
employment is (x) at the time of the Acquisition terminated by the Company
without cause or (y) terminated by any Successor To The Business without Cause
or the Employee terminates his employment for Good Reason (as defined in the
Employment Agreement) and, in any such event, the Employee signs a comprehensive
release in the form and of a scope acceptable to the Company, then the options
granted hereby will become exercisable in full on the date of the Acquisition
(in the case of (i)) or such termination (in the case of (ii)).

                      (b) ACQUISITION DEFINED. An "Acquisition" shall mean: (x)
any merger or consolidation after which the voting securities of the Company
outstanding immediately prior thereto represent (either by remaining outstanding
or by being converted into voting securities of the surviving or acquiring
entity) less than 50% of the combined voting power of the voting securities of
the Company or such surviving or acquiring entity outstanding immediately after
such event; or (y) any sale of all or substantially all of the assets or capital
stock of the Company (other than in a spin-off or similar transaction); or (z)
any other acquisition of the business of the Company, as determined by the
Board.

                      (c) POOLING-OF-INTERESTS-ACCOUNTING. If the Company
proposes to engage in an Acquisition intended to be accounted for as a
pooling-of-interests, and in the event that the provisions of this option, or
any actions of the Board taken in connection with such Acquisition, are
determined by the Company's or the acquiring
<PAGE>   5
company's independent public accountants to cause such Acquisition to fail to be
accounted for as a pooling-of-interests, then such provisions or actions shall
be amended or rescinded by the Board, without the consent of the Optionee, to be
consistent with pooling-of-interests accounting treatment for such Acquisition
if, and to the extent that, such recision would result in such Acquisition being
accounted for on a pooling-of-interests basis.

           14. ARBITRATION. Any dispute, controversy, or claim arising out of,
in connection with, or relating to the performance of this Agreement or its
termination shall be settled by arbitration in the Commonwealth of
Massachusetts, pursuant to the rules then obtaining of the American Arbitration
Association. Any award shall be final, binding and conclusive upon the parties
and a judgment rendered thereon may be entered in any court having jurisdiction
thereof.

           15. PROVISION OF DOCUMENTATION TO OPTIONEE. By signing this Agreement
the Optionee acknowledges receipt of a copy of this Agreement.

           16. MISCELLANEOUS.

                      (a) NOTICES. All notices hereunder shall be in writing and
           shall be deemed given when sent by certified or registered mail,
           postage prepaid, return receipt requested, if to the Optionee, to the
           address set forth on the cover pages hereof or at the address shown
           on the records of the Company, and if to the Company, to the
           Company's principal executive offices, attention of the Corporate
           Secretary.

                      (b) ENTIRE AGREEMENT; MODIFICATION. This Agreement and the
           Employment Agreement constitute the entire agreement between the
           parties relative to the subject matter hereof, and supersedes all
           proposals, written or oral, and all other communications between the
           parties relating to the subject matter of this Agreement. This
           Agreement may be modified, amended or rescinded only by a written
           agreement executed by both parties.

                      (c) FRACTIONAL SHARES. If this option becomes exercisable
           for a fraction of a share because of the adjustment provisions
           contained herein, such fraction shall be rounded down.

                      (d) NO RIGHTS AS STOCKHOLDER. The Optionee shall not have
           any rights as a stockholder with respect to any shares of Common
           Stock for which this option is exercisable until such Optionee
           becomes the record holder of such shares of Common Stock.

                      (e) NO OBLIGATION OF CONTINUED EMPLOYMENT. This Agreement
           imposes no obligation on the Company or Related Corporation to
           continue the employment of the Employee. The Company expressly
           reserves the right any time to dismiss or terminate its relationship
           with the Employee free from any liability or claim under this
           Agreement.

                      (f) ISSUANCES OF SECURITIES; CHANGES IN CAPITAL STRUCTURE.
           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
           subject to this option. No adjustments need be made for dividends
           paid in cash or in property other than securities of the Company. If
           there shall be any change in the Common Stock of the Company through
           merger, consolidation, reorganization, recapitalization, stock
           dividend, stock split, combination or exchange of shares, spin-off,
           split-up or other similar change in capitalization or event, the
           restrictions contained in this Agreement shall apply with equal force
           to additional and/or substitute securities, if any, received by the
           Optionee in exchange for, or by virtue of his or her ownership of,
           Option Shares, except as otherwise determined by the Board.

                      (g) DISSOLUTION OR LIQUIDATION. In the event of the
           proposed dissolution or liquidation of the Company, then the Board
           shall, as to outstanding options, at its discretion provide, upon
           written notice to the Optionee (i) that all options must be
           exercised, to the extent then exercisable, within a specified
<PAGE>   6
           number of days of the date of such notice, at the end of which
           period, the options shall terminate or (ii) that such options
           (including those which have not yet vested) shall be exercisable
           within a specified number of days of such notice, at the end of which
           period the options shall terminate.

                      (h) SEVERABILITY. The invalidity, illegality or
           unenforceability of any provision of this Agreement shall in no way
           affect the validity, legality or enforceability of any other
           provision.

                      (i) SUCCESSORS AND ASSIGNS. This Agreement shall be
           binding upon and inure to the benefit of the parties hereto and their
           respective successors and assigns, subject to the limitations set
           forth in Section 9 hereof.

                      (j) GOVERNING LAW. This Agreement shall be governed by and
           interpreted in accordance with the laws of the Commonwealth of
           Massachusetts, without giving effect to the principles of the
           conflicts of laws thereof.