<PAGE>
 
                                                                           10.41
                                                                  EXECUTION COPY



                             DATED        1998
                             -----------------



                          (1) CHIREX (DUDLEY) LIMITED

                             (2) JOHN EDWARD WEIR



                         COMPROMISE AGREEMENT PURSUANT
                   TO (INTER ALIA) SECTION 77(4)(AA) OF THE
                         SEX DISCRIMINATION ACT 1975,
                          SECTION (72)(4)(AA) OF THE
                           RACE RELATIONS ACT 1976,
                               SECTION 9 OF THE
                      DISABILITY DISCRIMINATION ACT 1995
                         AND SECTION 203(2)(F) OF THE
                          EMPLOYMENT RIGHTS ACT 1996

                                       1
<PAGE>
 
                             COMPROMISE AGREEMENT
                             --------------------

THIS AGREEMENT is made on the [             ] of July 1998 BETWEEN CHIREX
(DUDLEY) LIMITED of Dudley, Cramlington, Northumberland ("the Company") and JOHN
EDWARD WEIR (" Mr Weir").

This Agreement relates to the termination of Mr Weir's employment with the
Company on July 15, 1998 ("the Termination Date") by reason of resignation.


IT IS AGREED that:-


1. The Company will pay Mr Weir


   1.1  all accrued salary and holiday pay of Mr Weir up to the Termination Date
        after deductions of tax and National Insurance.

   1.2  The sum of (Pounds)33,000 as compensation for loss of employment, which
        payment will be paid to Mr Weir in six equal monthly instalments on the
        27th of each month through the Company's payroll commencing on 27th July
        1998.

   1.3  The sum of (Pounds)1200 in lieu of payment for private fuel, which
        payment will be subject to deductions for tax and national insurance,
        and will be paid forthwith following Mr Weir's signing this Agreement.


   2.1  Mr Weir shall be entitled to continue as a member of the ChiRex private
        health insurance scheme for a period of one year until July 14, 1999.

                                       2
<PAGE>
 
2.2  The Company will gift to Mr Weir his company car within seven days of the
     termination date.

3.1  The Company and Mr Weir consider that the payment referred to in clause 1
     above can be made free of tax. However if it is subsequently determined
     that the Inland Revenue is entitled to income tax or national insurance
     contributions are due in respect of the payment referred to in clause 1,
     then Mr Weir will be responsible for such tax and national insurance
     contributions and subject to the provisions of this clause he will
     indemnify the Company against such tax and national insurance contributions
     as it may be called upon to pay and does pay.

3.2  The Company will be responsible for and will pay to the Inland Revenue such
     tax and national insurance contributions as are assessed by the Inland
     Revenue as payable in respect of the benefits described in clause 2 above.

4.   Mr Weir agrees to accept the payment and receipt of the sums and other
     benefits stipulated in Clause 1 above in full and final settlement of all
     claims of whatever nature (including, but not limited to any claims under
     English law and/or European Community Law and/or U.S. Law) which he may
     have against the Company and/or all companies which are for the time being
     either a holding company of the Company or a subsidiary or associated
     company of either the Company or any such holding company ("Group" or
     "Group Companies") arising out of his Contract of Employment and/or the
     termination thereof whether pursuant to statute or at common law or
     otherwise howsoever including but not limited to any claims for wrongful
     dismissal, unfair dismissal, redundancy, breach of contract, or under the
     Sex Discrimination Act 1975, the Race Relations Act 1976, the Disability
     Discrimination Act 1995 or the Employment Rights Act 1996 ("the 1996 Act").

                                       3
<PAGE>
 
5.   The Company agrees that in consideration of Mr Weir entering into this
     Agreement that neither it nor any of the Group Company will make any claim
     against him arising out of his employment with the Company.

6.   Weir HEREBY AGREES that upon the Termination Date he shall resign from
     office as a Director of the Company such resignation to be in the form
     (mutatis mutandis) of the letter attached as the First Schedule hereto.

7.   Mr Weir agrees that he will not disclose (whether directly or indirectly)
     the details of this settlement or the circumstances relating to the
     termination of his employment to any third party without the consent in
     writing of the Company having first been obtained except for the purpose of
     taking professional advice or in respect of any necessary disclosure to the
     statutory authorities.

8.   The Company and Mr Weir undertake that they will not whether directly or
     indirectly make, publish or otherwise communicate any disparaging or
     derogatory statements whether in writing or otherwise concerning the other
     including in the case of Mr Weir concerning the Company or any of its
     Associated Companies or any of its or their officers or employees to any
     third party including but not limited to any person firm or company who was
     at any time during Mr Weir's employment with the Company, a customer or
     supplier of the Company. This term is of the essence of the contract.

9.   Mr Weir undertakes that on the July 15, 1998 he will return to the Company
     any property which is in his possession which belongs to the Company
     (except for the said motor car) and in particular he will return all
     documentation relating to the business of the Company or any subsidiary or
     associated company and he will not retain copies thereof.

10.  Mr Weir agrees to remain bound by the post-termination restraints set out
     in paragraphs 8 and 9 of the Service Agreement between Crossco (157)
     Limited and Mr Weir which

                                       4
<PAGE>
 
     applied to Mr Weir's employment with the Company dated March 11, 1996 as if
     the same were repeated herein

11.  Subject to Mr Weir's prompt delivery of his Chirex share certificates to Ms
     Beth Hecht, General Counsel, ChiRex, 300 Atlantic Street, Suite 402,
     Stamford, CT06901, fax number 203.425.9996 and SEC rules she will arrange
     to have the restrictive legends lifted, such lifting to have effect 90 days
     from July 15, 1998.

12.  Mr Weir shall be entitled to exercise all and any of his vested stock
     options which have vested as of July 15 1998. Such exercise of vested
     options must occur on or before October 15, 1998. After October 15, 1998,
     all unexercised vested options shall become void.

13.  Mr Weir represents and warrants that:-

     (a)  He has received independent legal advice from a Qualified Lawyer as to
          the terms and effect of this Agreement and in particular its effect on
          his ability to pursue any rights that he may have before any
          Industrial Tribunal or Court. The name of the Qualified Lawyer who has
          advised Mr Weir is John Martin solicitor, of Norham House, New Bridge
          Street, Newcastle upon Tyne ("the Qualified Lawyer")

     (b)  Mr Weir has been advised by the Qualified Lawyer that there is in
          force and was at the time when he received the advice referred to
          above a policy of insurance covering, or cover under the Solicitors
          Indemnity Fund for the risk of a claim by him in respect of loss
          arising in consequence of that advice.

16.  A true copy of a letter dated July  1998 from the Qualified Lawyer to the
     Company's solicitors is attached as the Second Schedule hereto.

17.  The Company and Mr Weir agree and acknowledge that the statutory conditions
     regulating compromise agreements are intended to and have been satisfied.

18.  The Company will pay Mr Weir's solicitor's reasonable legal fees of F-500
     (plus VAT) in connection with this Agreement within fourteen days of
     receipt of the relevant invoice

                                       5
<PAGE>
 
     from Mr Weir's solicitors, the relevant invoice to be sent to Beth Hecht as
     aforesaid. The parties acknowledge that the above legal fees have been
     exclusively incurred in connection with the termination of Mr Weir's
     employment.

SIGNED for and on behalf of
CHIREX (DUDLEY) LIMITED
by [              ]


Dated:


SIGNED by MR WEIR

Dated:

                                       6
<PAGE>
 
THE FIRST SCHEDULE REFERRED TO ABOVE
------------------------------------

The Board of Directors
Chirex (Dudley) Ltd



                                                               1998

Gentlemen

I hereby resign from offices as Director of Chirex (Dudley) Limited and such
resignation to take effect when accepted by you.

I confirm that I have no claims against the company arising from or connected
with the above officeholdings at the termination thereof.

Yours faithfully

                                       7
<PAGE>
 
                     THE SECOND SCHEDULE REFERRED TO ABOVE
                     -------------------------------------

                                                                   [      ]1998


Short Richardson & Forth
4 Mosley Street
Newcastle upon Tyne
NE1 1SR

Your ref:

Our ref:

Dear Sirs

RE: MR WEIR AND CHIREX LIMITED
------------------------------

We write further to the Compromise Agreement under (inter alia) section
77(4)(aa) of the Sex Discrimination Act 1975, Section 72(4)(aa) of the Race
Relations Act 1976, Section 9 of the Disability Discrimination Act 1995 and
section 203(2)(f) of the Employment Rights Act 1996 proposed between Mr Weir and
Chirex Limited ("the Proposed Compromise Agreement").

This letter is to confirm that Mr Weir has been advised by [
], [a solictor in the employment] of this firm.

It is also confirmed that at the date hereof and at all times during which [
] has advised Mr Weir on the subject matter of the Proposed Compromise Agreement
and the legal effect of the same ("the Relevant Times") [he/she) is and has been
a Solicitor of the Supreme Court holding a practising certificate entitling
[him/her] to practise as such.

We further confirm that at the Relevant Times [       ] has not been acting in
this
matter for Chirex Limited or any associated company or associated employer of
its.

In view of what we say above, [              ] is a "qualified lawyer" and
"independent" of Chirex Limited having regard to the definitions given to those
words by section 77(4B) of the Sex Discrimination Act 1975, section 72(4B) of
the Race Relations Act 1976, section 9 of the Disability Discrimination Act
1995, section 203(4) of the Employment Rights Act 1996 and all and any other
statutory provisions of similar effect.

We also confirm that [      ] has given independent legal advice to Mr
Weir as to the terms and effect of the Proposed Compromise Agreement, and, in
particular, as to its effect on Mr Weir's ability to exercise any rights which
he has or may have to pursue a complaint against Chirex Limited before the
Industrial Tribunal in respect of which a Conciliation Officer is authorised to
act including (but not limited to) any complaint that Chirex Limited committed
an act of discrimination against him which was unlawful by virtue of Part II of
the Sex Discrimination Act 1975 or by virtue of Part II of the Race Relations
Act 1976 or by virtue of Part II of the Disability Discrimination Act 1995, that
it unfairly dismissed him in contravention of the provisions of Chapter 1 of
Part X to the Employment Rights Act 1996 or that it made any deduction from his
wages or received any payment from him in contravention of section 13(1) or
section 15(l) of that Act.

                                       8
<PAGE>
 
During the Relevant Times, there has been in force a policy of insurance
covering the risk of a claim by Mr Weir in respect of loss arising in
consequence of the advice given to him by [       ]. For the avoidance of doubt,
reference to "a policy of insurance" is to a "top up" insurance policy over and
above the indemnity cover provided by or through the Solicitors Indemnity Fund.

We confirm that this letter may be annexed to the Proposed Compromise Agreement.

Yours faithfully

                                       9