Document:

EX-10.1

EMPLOYMENT AGREEMENT

THIS EMPLOYMENT AGREEMENT (the “Agreement”), is dated as of May 4, 2006 (the
“Effective Date”), by and between NEOSE TECHNOLOGIES, INC. (the “Company”) and GEORGE J.
VERGIS, PH.D. (the “Executive”).

Background

The Executive has been promoted by the Company’s Board of Directors (the “Board”) to serve as
the President and Chief Executive Officer of the Company, effective May 4, 2006, and has been
appointed by the Board to serve as a director of the Company. The Executive and the Company have
agreed to the terms and conditions of his employment in that role, as set forth herein.

Terms

NOW, THEREFORE, in consideration of the foregoing and the mutual covenants and promises
contained herein, and intending to be bound hereby, the parties agree as follows:

1. Employment.

1.1. Term. The Company agrees to employ the Executive in accordance with the terms of
this Agreement and the Executive agrees to accept such continued employment, effective on the
Effective Date and continuing until terminated pursuant to Section 4 hereof (the “Term”).

1.2. Positions. During the Term, Executive will serve as President and Chief
Executive Officer of the Company, reporting directly to the Board. The Board agrees to nominate
the Executive for reelection to the Board at each annual meeting of the Company’s stockholders
occurring during the Term and at which the Executive’s term as a director is scheduled to expire.

1.3. Duties. The Executive will perform such duties and functions as are customarily
performed by the president and chief executive officer of an enterprise the size and nature of the
Company, including the duties and functions from time to time assigned to him by the Board.
Without limiting the generality of the foregoing, the Executive will be responsible for all aspects
of the Company’s performance, including strategy, research and development, business development,
sales and marketing, operations, manufacturing, technology development and licensing, corporate
development, information management, finance, legal, patent, regulatory, human resources, investor
relations and corporate communications.

1.4. Place of Performance. The Executive shall perform his services hereunder at the
principal executive offices of the Company, which are currently located in Horsham, Pennsylvania;
provided, however, that the Executive will be required to travel from time to time for business
purposes.

1.5. Time Devoted to Employment. The Executive will devote his best efforts and
substantially all of his business time and services to the performance of his duties under this
Agreement. Notwithstanding the foregoing, the Executive may engage in charitable, community
service and industry association activities, and, with the approval of the Board (which approval
will not be unreasonably withheld), may serve as a member of boards of directors of other companies
or organizations, which, in the judgment of the Board, will not present any conflict of interest
with the Company, so long as those activities do not interfere with the performance of his duties
under this Agreement.

2. Compensation, Benefits and Expense Reimbursements.

2.1. Base Salary. The Executive shall receive an initial annual salary of $350,000
(the “Base Salary”), paid semi-monthly or otherwise in accordance with the Company’s
customary payroll practices, as in effect from time to time. Future salary reviews will be
undertaken by the Board of Directors annually.

2.2. Bonus. The Executive will be eligible to receive an annual bonus (the
“Annual Bonus”) for each completed calendar year during the Term. The target amount of the
Annual Bonus is 75% of the Base Salary for the applicable calendar year. The specific goals and
objectives that must be met to receive the target bonus will be established by mutual agreement by
the Board and the Executive within 90 days following the commencement of each calendar year during
the Term, and within 30 days following the Effective Date for the initial, partial calendar year of
the Term . The Company will endeavor to pay the Annual Bonus, if any, within two and one-half
months following the end of the calendar year to which the Annual Bonus relates. Provided the
Executive remains employed by the Company through March 15, 2007 (or, if sooner, the actual date of
payment by the Company of annual bonuses to senior executives), the Executive’s Annual Bonus with
respect to the 2006 calendar year will not be less than $105,000.

2.3. Equity Incentive. The Board has authorized the grant to the Executive, effective
February 15, 2006 (“Grant Date”), of options to purchase 300,000 shares of the Company’s common
stock (the “Stock Option”) with a per share exercise price equal to the fair market value
of a share of common stock on the Grant Date. The Stock Option will vest in four equal, annual
installments commencing on February 15, 2007, the first anniversary of the Grant Date, be reflected
in a stock option agreement identical in all material respects to the Company’s Form Stock Option
Agreement and be non-qualified stock options. The Stock Option will be subject in all respects to
the terms of the Company’s 2004 Equity Incentive Plan.

2.4. Expenses. The Executive will be entitled to reimbursement by the Company for all
expenses reasonably incurred by him in connection with the performance of his duties, including,
without limitation, travel and entertainment expenses reasonably related to the business of the
Company, in accordance with the policies and procedures established from time to time by the
Company.

2.5. Other Benefits. The Executive will be entitled to participate in any benefit
plans, policies or arrangements sponsored or maintained by the Company from time to time for its
senior executive officers (which benefits, as of this date, include the right to participate in the
Company’s 401(k), employee stock purchase, medical, and dental plans, and coverage under the
Company’s group life and disability insurance policies). Notwithstanding the foregoing, the
Executive’s eligibility for and participation in any of the Company’s employee benefit plans,
policies or arrangements will be subject to the terms and conditions of such plans, policies or
arrangements. Moreover, subject to the terms and conditions of such plans, policies or
arrangements, the Company may amend, modify or terminate such plans, policies or arrangements at
any time for any reason. In addition, the cost of the Executive’s annual physical examination
shall be borne by the Company, to the extent not covered by the Company’s medical plan.

2.6. Vacations. In addition to holidays observed by the Company, the Executive shall
be entitled to four (4) weeks paid vacation time during each year of employment consistent with
Company policies, as in effect from time to time.

3. [Reserved]

4. Termination.

4.1. In General. The Company may terminate the Executive’s employment at any time.
The Executive may terminate his employment at any time, provided that, before the Executive may
voluntarily terminate his employment with the Company other than for Good Reason, he must provide
90 days prior written notice (or such shorter notice as is acceptable to the Company) to the
Company. Upon any termination of the Executive’s employment with the Company for any reason: (i)
the Executive (unless otherwise requested by the Board) concurrently will resign all officer or
director positions he holds with the Company, its subsidiaries or affiliates, and (ii) the Company
will pay to the Executive all accrued but unpaid Base Salary through the date of termination, and
(iii) except as explicitly provided in Sections 4, 6 or 7, or otherwise pursuant to COBRA, all
compensation and benefits will cease and the Company will have no further liability or obligation
to the Executive. The foregoing will not be construed to limit the Executive’s right to payment or
reimbursement for claims incurred prior to the date of such termination under any insurance
contract funding an employee benefit plan, policy or arrangement of the Company in accordance with
the terms of such insurance contract.

4.2. Termination without Cause or for Good Reason.

4.2.1. If the Executive’s employment by the Company ceases due to a termination by the Company
without Cause or a resignation by the Executive for Good Reason, then, in addition to the payments
and benefits provided for in Section 4.1 above and subject to Section 8 below: (a) the Company will
pay to the Executive on the date of such termination a cash amount equal to the sum of (i) one year
of the Executive’s Base Salary as in effect on such date, and (ii) the target Annual Bonus amount
applicable for the calendar year in which the termination occurs, (b) to the extent not previously
paid, the Company will pay to the Executive any Annual Bonus payable with respect to a calendar
year that ended prior to that termination, (c) all outstanding stock options then held by the
Executive (including the Stock Option) will immediately become vested and exercisable with respect
to that number of additional shares of the Company’s common stock with respect to which such stock
options would have become vested and exercisable had the Executive remained continuously employed
by the Company for an additional 12 months following his termination of employment and will remain
exercisable until the end of the calendar year in which such options would have otherwise expired
(or, if later, 2 1/2 months following the date such options would have otherwise expired), and (d)
the Company will pay to the Executive the additional amount, if any, payable pursuant to Section 7
below; provided that if the Company’s obligation to make the payments provided for in this Section
4.2.1 arises due to a termination of the Executive’s employment due to his death or Disability (as
defined below), the cash payments described in clauses (a) and (b) of this Section 4.2.1 will be
offset by the amount of benefits paid to the Executive (or his representative(s), heirs, estate or
beneficiaries) pursuant to the life insurance or long-term disability plans, policies or
arrangements of the Company by virtue of his death or that Disability (including, for this purpose,
only that portion of such life insurance or disability benefits funded by the Company or by premium
payments made by the Company).

4.2.2. For purposes of this Agreement, the Executive’s employment will be deemed to have been
terminated without “Cause” if his employment is terminated as a result of his death or
Disability or is terminated by the Company other than as a result of fraud, embezzlement, or any
other illegal act committed intentionally by the Executive in connection with his employment or the
performance of his duties as an officer or director of the Company. For purposes of this
Agreement, “Disability” means the Executive’s inability, by reason of any physical or
mental impairment, to substantially perform his regular duties as contemplated by this Agreement,
as determined by the Board in its sole discretion (after affording the Executive the opportunity to
present his case), which inability is reasonably contemplated to continue for at least one year
from its commencement and at least 90 days from the date of such determination.

4.2.3. For purposes of this Agreement, “Good Reason” means, without the Executive’s
prior written consent, any of the following:

(a) a change in the Executive’s title (not including the election of the Executive as Chairman
of the Board);

(b) a reduction in the Executive’s authority, duties or responsibilities, or the assignment to
the Executive of duties that are inconsistent, in a material respect, with Executive’s position;

(c) the relocation of the Company’s headquarters more than 15 miles from Horsham,
Pennsylvania, unless such move reduces Executive’s commuting time;

(d) a reduction in the Base Salary or in the target amount, expressed as a percentage of Base
Salary, of the Annual Bonus; or

(e) the Company’s failure to pay or make available any material payment or benefit due under
this Agreement or any other material breach by the Company of this Agreement.

However, the foregoing events or conditions will constitute Good Reason only if the Executive
provides the Company with written objection to the event or condition within 60 days following the
Executive’s knowledge of the occurrence thereof, the Company does not reverse or otherwise cure the
event or condition within 30 days of receiving that written objection and the Executive resigns his
employment within 90 days following the expiration of that cure period.

5. Restrictive Covenants. As consideration for all of the payments to be made to the
Executive pursuant to Sections 2, 4 and 6 of this Agreement, as well as for any equity incentive
awards that the Executive may receive from the Company, the Executive agrees to be bound by the
provisions of this Section 5 (the “Restrictive Covenants”). These Restrictive Covenants
will apply without regard to whether any termination of the Executive’s employment is initiated by
the Company or the Executive, and without regard to the reason for that termination.

5.1. Covenant Not To Compete. The Executive covenants that, during the period
beginning on the Effective Date and ending on the first anniversary of the termination of the
Executive’s employment with the Company for any reason (the “Restricted Period”), he will
not (except in his capacity as an employee or director of the Company) do any of the following,
directly or indirectly, anywhere in the world:

5.1.1. engage or participate in any business competitive with the Business (as defined below);

5.1.2. become interested in (as owner, stockholder, lender, partner, co-venturer, director,
officer, employee, agent or consultant) any person, firm, corporation, association or other entity
engaged in any business competitive with the Business. Notwithstanding the foregoing, the
Executive may hold up to 4.9% of the outstanding securities of any class of any publicly-traded
securities of any company;

5.1.3. engage in any business, or solicit or call on any customer, supplier, licensor,
licensee, contractor, agent, representative, advisor, strategic partner, distributor or other
person with whom the Company shall have dealt or any prospective customer, supplier, licensor,
licensee, contractor, agent, representative, advisor, strategic partner, distributor or other
person that the Company shall have identified and solicited at any time during the Executive’s
employment by the Company for a purpose competitive with the Business;

5.1.4. influence or attempt to influence any employee, consultant, customer, supplier,
licensor, licensee, contractor, agent, representative, advisor, strategic partner, distributor or
other person to terminate or modify any written or oral agreement, arrangement or course of dealing
with the Company; or

5.1.5. solicit for employment or employ or retain (or arrange to have any other person or
entity employ or retain) any person who has been employed or retained by the Company within the 12
months preceding the termination of the Executive’s employment with the Company for any reason.

5.2. Confidentiality. The Executive recognizes and acknowledges that the Proprietary
Information (as defined below) is a valuable, special and unique asset of the business of the
Company. As a result, both during the Term and thereafter, the Executive will not, without the
prior written consent of the Company, for any reason either directly or indirectly divulge to any
third-party or use for his own benefit, or for any purpose other than the exclusive benefit of the
Company, any Proprietary Information; provided, however, that the Executive may during the Term
disclose Proprietary Information to third parties as may be necessary or appropriate to the
effective and efficient discharge of his duties as an employee hereunder (provided that the third
party recipient has signed the Company’s then-approved confidentiality or similar agreement) or as
such disclosures may be required by law. If the Executive or any of his representatives becomes
legally compelled to disclose any of the Proprietary Information, the Executive will provide the
Company with prompt written notice so that the Company may seek a protective order or other
appropriate remedy. The non-disclosure and non-use obligations with respect to Proprietary
Information set forth in this Section 5.2 shall not apply to any information that is in or becomes
part of the public domain through no improper act on the part of the Executive.

5.3. Property of the Company.

5.3.1. Proprietary Information. All right, title and interest in and to Proprietary
Information will be and remain the sole and exclusive property of the Company. The Executive will
not remove from the Company’s offices or premises any documents, records, notebooks, files,
correspondence, reports, memoranda or similar materials of or containing Proprietary Information,
or other materials or property of any kind belonging to the Company unless necessary or appropriate
in the performance of his duties to the Company. If the Executive removes such materials or
property in the performance of his duties, the Executive will return such materials or property to
their proper files or places of safekeeping as promptly as possible after the removal has served
its specific purpose. The Executive will not make, retain, remove and/or distribute any copies of
any such materials or property, or divulge to any third person the nature of and/or contents of
such materials or property or any other oral or written information to which he may have access or
become familiar in the course of his employment, except to the extent necessary in the performance
of his duties. Upon termination of the Executive’s employment with the Company, he will leave with
the Company or promptly return to the Company all originals and copies of such materials or
property then in his possession.

5.3.2. Intellectual Property. The Executive agrees that all the Intellectual Property
(as defined below) will be considered “works made for hire” as that term is defined in Section 101
of the Copyright Act (17 U.S.C. § 101) and that all right, title and interest in such Intellectual
Property will be the sole and exclusive property of the Company. To the extent that any of the
Intellectual Property may not by law be considered a work made for hire, or to the extent that,
notwithstanding the foregoing, the Executive retains any interest in the Intellectual Property, the
Executive hereby irrevocably assigns and transfers to the Company any and all right, title, or
interest that the Executive may now or in the future have in the Intellectual Property under
patent, copyright, trade secret, trademark or other law, in perpetuity or for the longest period
otherwise permitted by law, without the necessity of further consideration. The Company will be
entitled to obtain and hold in its own name all copyrights, patents, trade secrets, trademarks and
other similar registrations with respect to such Intellectual Property. The Executive further
agrees to execute any and all documents and provide any further cooperation or assistance
reasonably required by the Company, at the Company’s sole cost and expense, to perfect, maintain or
otherwise protect its rights in the Intellectual Property. If the Company is unable after
reasonable efforts to secure the Executive’s signature, cooperation or assistance in accordance
with the preceding sentence, whether because of the Executive’s incapacity or any other reason
whatsoever, the Executive hereby designates and appoints the Company or its designee as the
Executive’s agent and attorney-in-fact, to act on his behalf, to execute and file documents and to
do all other lawfully permitted acts necessary or desirable to perfect, maintain or otherwise
protect the Company’s rights in the Intellectual Property. The Executive acknowledges and agrees
that such appointment is coupled with an interest and is therefore irrevocable.

5.4. Definitions. For purposes of this Agreement, the following terms have the
meanings defined below:

5.4.1. “Business” means research, development, manufacture, supply, marketing,
licensing, use and sale of biologic, pharmaceutical and therapeutic materials and products and
related process technology including, without limitation, research, development, manufacture,
supply, marketing, licensing, use and sale of products and technology directed to (a) the enzymatic
synthesis of complex carbohydrates for use in food, cosmetic, therapeutic, consumer and industrial
applications, (b) enzymatic synthesis or modification of the carbohydrate portion of proteins or
lipids, (c) carbohydrate-based therapeutics and (d) the development of protein therapeutics using
siallylation, fucosylation, glycosylation, GlycoPEGylationTM, or GlycoconjugationTM .

5.4.2. “Intellectual Property” means (a) all inventions (whether patentable or
unpatentable and whether or not reduced to practice), all improvements thereto, and all patents and
patent applications claiming such inventions, (b) all trademarks, service marks, trade dress,
logos, trade names, fictitious names, brand names, brand marks and corporate names, together with
all translations, adaptations, derivations, and combinations thereof and including all goodwill
associated therewith, and all applications, registrations, and renewals in connection therewith,
(c) all copyrightable works, all copyrights, and all applications, registrations, and renewals in
connection therewith, (d) all mask works and all applications, registrations, and renewals in
connection therewith, (e) all trade secrets (including research and development, know-how,
formulas, compositions, manufacturing and production processes and techniques, methodologies,
technical data, designs, drawings and specifications), (f) all computer software (including data,
source and object codes and related documentation), (g) all other proprietary rights, (h) all
copies and tangible embodiments thereof (in whatever form or medium), or similar intangible
personal property which have been or are developed or created in whole or in part by the Executive
(i) at any time and at any place while the Executive is employed by Company and which, in the case
of any or all of the foregoing, are related to and used in connection with the business of the
Company, or (ii) as a result of tasks assigned to the Executive by the Company.

5.4.3. “Proprietary Information” means any and all information of the Company or of
any subsidiary or affiliate of the Company. Such Proprietary Information shall include, but shall
not be limited to, the following items and information relating to the following items: (a) all
intellectual property and proprietary rights of the Company (including without limitation
Intellectual Property) (b) computer codes or instructions (including source and object code
listings, program logic algorithms, subroutines, modules or other subparts of computer programs and
related documentation, including program notation), computer processing systems and techniques, all
computer inputs and outputs (regardless of the media on which stored or located), hardware and
software configurations, designs, architecture and interfaces, (c) business research, studies,
procedures and costs, (d) financial data, (e) distribution methods, (f) marketing data, methods,
plans and efforts, (g) the identities of actual and prospective customers, contractors and
suppliers, (h) the terms of contracts and agreements with customers, contractors and suppliers, (i)
the needs and requirements of, and the Company’s course of dealing with, actual or prospective
customers, contractors and suppliers, (j) personnel information, (k) customer and vendor credit
information, and (l) any information received from third parties subject to obligations of
non-disclosure or non-use. Failure by the Company to mark any of the Proprietary Information as
confidential or proprietary shall not affect its status as Proprietary Information under the terms
of this Agreement.

5.5. Acknowledgements. The Executive acknowledges that the Restrictive Covenants are
reasonable and necessary to protect the legitimate interests of the Company and its affiliates and
that the duration and geographic scope of the Restrictive Covenants are reasonable given the nature
of this Agreement and the position the Executive will hold within the Company. The Executive
further acknowledges that the Restrictive Covenants are included herein in order to induce the
Company to promote the Executive and that the Company would not have entered into this Agreement or
otherwise promoted the Executive in the absence of the Restrictive Covenants.

5.6. Remedies and Enforcement Upon Breach.

5.6.1. Specific Enforcement. The Executive acknowledges that any breach by him,
willfully or otherwise, of the Restrictive Covenants will cause continuing and irreparable injury
to the Company for which monetary damages would not be an adequate remedy. The Executive shall
not, in any action or proceeding to enforce any of the provisions of this Agreement, assert the
claim or defense that such an adequate remedy at law exists. In the event of any such breach by
the Executive, the Company shall have the right to enforce the Restrictive Covenants by seeking
injunctive or other relief in any court, without any requirement that a bond or other security be
posted, and this Agreement shall not in any way limit remedies of law or in equity otherwise
available to the Company.

5.6.2. Judicial Modification. If any court determines that any of the Restrictive
Covenants, or any part thereof, is unenforceable because of the duration or geographical scope of
such provision, such court shall have the power to modify such provision and, in its modified form,
such provision shall then be enforceable.

5.6.3. Accounting. If the Executive breaches any of the Restrictive Covenants, the
Company will have the right and remedy to require the Executive to account for and pay over to the
Company all compensation, profits, monies, accruals, increments or other benefits derived or
received by the Executive as the result of such breach. This right and remedy will be in addition
to, and not in lieu of, any other rights and remedies available to the Company under law or in
equity.

5.6.4. Enforceability. If any court holds the Restrictive Covenants unenforceable by
reason of their breadth or scope or otherwise, it is the intention of the parties hereto that such
determination not bar or in any way affect the right of the Company to the relief provided above in
the courts of any other jurisdiction within the geographic scope of such Restrictive Covenants.

5.6.5. Disclosure of Restrictive Covenants. The Executive agrees to disclose the
existence and terms of the Restrictive Covenants to any employer that the Executive may work for
during the Restricted Period.

5.6.6. Extension of Restricted Period. If the Executive breaches Section 5.1 in any
respect, the restrictions contained in that section will be extended for a period equal to the
period that the Executive was in breach.

6. Change in Control.

6.1. Certain Terminations Following a Change in Control. If the Executive’s
employment with the Company ceases within eighteen months following a Change in Control (as defined
below) as a result of a termination by the Company without Cause or a resignation by the Executive
for Good Reason, then:

6.1.1. the Restricted Period will be extended by one year;

6.1.2. subject to Section 8 and in lieu of the payments and benefits provided for in Section
4.2, (a) the Company will pay to the Executive on the date of such termination a cash amount equal
to the sum of (i) two years of the Executive’s Base Salary as in effect on such date, and (ii) two
times the target Annual Bonus amount applicable for the calendar year in which the termination
occurs, (b) to the extent not previously paid, the Company will pay to the Executive any Annual
Bonus payable with respect to a calendar year that ended prior to that termination, (c) all
outstanding stock options then held by Executive (including the Stock Option) will then become
fully vested and immediately exercisable and will remain exercisable until the end of the calendar
year in which such options would have otherwise expired (or, if later, 2 1/2 months following the
date such options would have otherwise expired), and (d) the Company will pay to the Executive the
additional amount, if any, payable pursuant to Section 7 below.

6.2. Definitions. For purposes of this Agreement, the term “Change in
Control” means a change in ownership or control of the Company effected through any of the
following transactions:

6.2.1. the direct or indirect acquisition by any person or related group of persons (other
than the Company or a person that directly or indirectly controls, is controlled by, or is under
common control with, the Company) of beneficial ownership (within the meaning of Rule 13d-3 of the
Securities Exchange Act of 1934, as amended) of securities possessing more than 50% of the total
combined voting power of the Company’s outstanding securities;

6.2.2. a change in the composition of the Board over a period of 36 months or less such that a
majority of the Board members ceases, by reason of one or more contested elections for Board
membership, to be comprised of individuals who either (a) have been board members continuously
since the beginning of such period, or (b) have been elected or nominated for election as Board
members during such period by at least a majority of the Board members described in clause (a) who
were still in office at the time such election or nomination was approved by the Board;

6.2.3. the consummation of any consolidation, share exchange or merger of the Company (a) in
which the stockholders of the Company immediately prior to such transaction do not own at least a
majority of the voting power of the entity which survives/results from that transaction, or (b) in
which a stockholder of the Company who does not own a majority of the voting stock of the Company
immediately prior to such transaction, owns a majority of the Company’s voting stock immediately
after such transaction; or

6.2.4. the liquidation or dissolution of the Company or any sale, lease, exchange or other
transfer (in one transaction or a series of related transactions) of all or substantially all the
assets of the Company, including stock held in subsidiary corporations or interests held in
subsidiary ventures.

7. Parachute Payments.

7.1. Generally. All amounts payable to the Executive under this Agreement will be
made without regard to whether the deductibility of such payments (considered together with any
other entitlements or payments otherwise paid or due to the Executive) would be limited or
precluded by Section 280G of the Code and without regard to whether such payments would subject the
Executive to the excise tax levied on certain “excess parachute payments” under Section 4999 of the
Code (the “Parachute Excise Tax”).

7.2. Gross-Up. If all or any portion of the payments or other benefits provided under
any section of this Agreement, either alone or together with any other payments and benefits which
the Executive receives or is entitled to receive from the Company or its affiliates (whether paid
or payable or distributed or distributable) pursuant to the terms of this Agreement or otherwise
pursuant to or by reason of any other agreement, policy, plan, program or arrangement, including
without limitation any stock option, stock appreciation right or similar right, or the lapse or
termination of any restriction on or the vesting or exercisability of any of the foregoing (the
“Payment”) would result in the imposition of a Parachute Excise Tax, the Executive will be entitled
to an additional payment (the “Gross-up Payment”) in an amount such that the net amount of the
Payment and the Gross-up Payment retained by the Executive after the calculation and deduction of
all excise taxes (including any interest or penalties imposed with respect to such taxes) on the
Payment and all federal, state and local income tax, employment tax and excise tax (including any
interest or penalties imposed with respect to such taxes) on the Gross-up Payment provided for in
this Section 7.2, and taking into account any lost or reduced tax deductions on account of the
Gross-up Payment, shall be equal to the Payment.

7.3. Measurements and Adjustments. The determination of the amount of the payments
and benefits paid and payable to the Executive and whether and to what extent payments under
Section 7.2 are required to be made will be made at the Company’s expense by an independent auditor
selected by mutual agreement of the Company and the Executive, which auditor shall provide
Executive and the Company with detailed supporting calculations with respect to its determination
within fifteen (15) business days of the receipt of notice from the Executive or the Company that
the Executive has received or will receive a payment that is potentially subject to the Parachute
Excise Tax. For the purposes of determining whether any payments will be subject to the Parachute
Excise Tax and the amount of such Parachute Excise Tax, such payments will be treated as “parachute
payments” within the meaning of section 280G of the Code, and all “parachute payments” in excess of
the “base amount” (as defined under section 280G(b)(3) of the Code) shall be treated as subject to
the Parachute Excise tax, unless and except to the extent that in the opinion of the accountants
such payments (in whole or in part) either do not constitute “parachute payments” or represent
reasonable compensation for services actually rendered (within the meaning of section 280G(b)(4) of
the Code) in excess of the “base amount,” or such “parachute payments” are otherwise not subject to
such Parachute Excise Tax. For purposes of determining the amount of the Gross-up Payment, if any,
the Executive shall be deemed to pay federal income taxes at the highest applicable marginal rate
of federal income taxation for the calendar year in which the gross-up payment is to be made and to
pay any applicable state and local income taxes at the highest applicable marginal rate of taxation
for the calendar year in which the gross-up payment is to be made, net of the maximum reduction in
federal income taxes which could be obtained from the deduction of such state or local taxes if
paid in such year (determined without regard to limitations on deductions based upon the amount of
the Executive’s adjusted gross income); and to have otherwise allowable deductions for federal,
state and local income tax purposes at least equal to those disallowed because of the inclusion of
the Gross-up Payment in the Executive’s adjusted gross income. Any Gross-up Payment shall be paid
by the Company at the time the Executive is entitled to receive the Payment. Any determination by
the auditor shall be binding upon the Company and the Executive.

7.4. In the event of any underpayment or overpayment to the Executive (determined after the
application of Section 7.2), the amount of such underpayment or overpayment will be, as promptly as
practicable, paid by the Company to the Executive or refunded by the Executive to the Company, as
the case may be, with interest at the applicable federal rate specified in Section 7872(f)(2) of
the Code.

8. Timing of Payments Following Termination.

8.1. Notwithstanding any provision of this Agreement, the payments and benefits described in
Sections 4.2, 6 and 7 are conditioned on the Executive’s execution and delivery to the Company of a
release substantially identical to that attached hereto as Exhibit I in a manner consistent
with the requirements of the Older Workers Benefit Protection Act (the “Mutual Release”).
The amounts described in Sections 4.2.1 and 6.1.2 will be paid in a lump sum, on the eighth day
following the Executive’s execution and delivery of the Mutual Release (provided that the Mutual
Release has not been revoked by the Executive). The Company covenants that if the Executive
executes the Mutual Release, the Company will also execute the Mutual Release.

8.2. IRC Section 409A. The Company and the Executive agree to exercise commercially
reasonable efforts to apply the terms of this Agreement in a manner consistent with the
requirements of Section 409A of the Code or to adjust the terms of this Agreement to the extent
necessary to avoid the application of additional taxes and penalties under Section 409A of the
Code.

9. Miscellaneous.

9.1. No Liability of Officers and Directors for Severance Upon Insolvency.
Notwithstanding any other provision of the Agreement and intending to be bound by this provision,
the Executive hereby (a) waives any right to claim payment of amounts owed to him, now or in the
future, pursuant to this Agreement from directors or officers of the Company if the Company becomes
insolvent, and (b) fully and forever releases and discharges the Company’s officers and directors
from any and all claims, demands, liens, actions, suits, causes of action or judgments arising out
of any present or future claim for such amounts.

9.2. Other Agreements. The Executive represents and warrants to the Company that
there are no restrictions, agreements or understandings whatsoever to which he is a party that
would prevent or make unlawful his execution of this Agreement, that would be inconsistent or in
conflict with this Agreement or Executive’s obligations hereunder, or that would otherwise prevent,
limit or impair the performance by Executive of his duties under this Agreement.

9.3. Successors and Assigns. The Company may assign this Agreement to any successor to
all or substantially all of its assets and business by means of liquidation, dissolution, merger,
consolidation, transfer of assets, or otherwise. The duties of the Executive hereunder are
personal to the Executive and may not be assigned by him.

9.4. Governing Law. This Agreement shall be governed by and construed in accordance
with the laws of the Commonwealth of Pennsylvania without regard to the principles of conflicts of
laws.

9.5. Enforcement. Any legal proceeding arising out of or relating to this Agreement
will be instituted in the United States District Court for the Eastern District of Pennsylvania, or
if that court does not have or will not accept jurisdiction, in any court of general jurisdiction
in the Commonwealth of Pennsylvania, and the Executive and the Company hereby consent to the
personal and exclusive jurisdiction of such court(s) and hereby waive any objection(s) that they
may have to personal jurisdiction, the laying of venue of any such proceeding and any claim or
defense of inconvenient forum.

9.6. Waivers; Separability. The waiver by either party hereto of any right hereunder
or any failure to perform or breach by the other party hereto shall not be deemed a waiver of any
other right hereunder or any other failure or breach by the other party hereto, whether of the same
or a similar nature or otherwise. No waiver shall be deemed to have occurred unless set forth in a
writing executed by or on behalf of the waiving party. No such written waiver shall be deemed a
continuing waiver unless specifically stated therein, and each such waiver shall operate only as to
the specific term or condition waived and shall not constitute a waiver of such term or condition
for the future or as to any act other than that specifically waived. If any provision of this
Agreement shall be declared to be invalid or unenforceable, in whole or in part, such invalidity or
unenforceability shall not affect the remaining provisions hereof which shall remain in full force
and effect.

9.7. Notices. All notices and communications that are required or permitted to be
given hereunder shall be in writing and shall be deemed to have been duly given when hand-delivered
or sent by first-class, registered or certified mail, nationally recognized overnight delivery
service, or by facsimile with a machine-generated confirmation (and with a confirmation copy sent
by one of the other methods listed above) to the other party at the address set forth below:

If to the Company, to:

Neose Technologies, Inc.

102 Witmer Road

Horsham PA 19044

Attn: General Counsel

Fax: 215-441-5896

With a copy to:

Pepper Hamilton LLP

3000 Two Logan Square

18th & Arch Streets

Philadelphia, PA 19103

Attn: Barry M. Abelson, Esquire

Fax: 215-981-4750

If to Executive, to:

George J. Vergis, Ph.D.

204 Weeks Pond Road

New Hope, PA 18938

With a copy to:

Edmonds & Co., P.C.

420 Fifth Avenue, 25th Floor

New York, New York 10018

Attn: Robert C. Edmonds, Esq.

Fax: 212-703-5440

or to such other address as may be specified in a notice given by one party to the other party
hereunder.

9.8. Entire Agreement; Amendments. As of the Effective Date, this Agreement and the
attached exhibits contain the entire agreement and understanding of the parties hereto relating to
the subject matter hereof, and merges and supersedes all prior and contemporaneous discussions,
agreements and understandings of every nature relating to the subject matter (including, without
limitation, that certain letter agreement between the Executive and the Company dated July 2, 2001
and that certain Change in Control Agreement between the Executive and the Company dated October
11, 2002). This Agreement may not be changed or modified, except by an Agreement in writing signed
by each of the parties hereto.

9.9. Withholding. The Company will withhold from any payments due to Executive, all
taxes, FICA or other amounts required to be withheld pursuant to any applicable law.

9.10. Headings Descriptive. The headings of sections and paragraphs of this Agreement
are inserted for convenience only and shall not in any way affect the meaning or construction of
any provision of this Agreement.

9.11. Counterparts. This Agreement may be executed in multiple counterparts, each of
which will be deemed to be an original, but all of which together will constitute but one and the
same instrument.

[This space left blank intentionally; signature page follows.]

1

IN WITNESS WHEREOF, the parties hereto have executed this Agreement on the date and year first
above written.

NEOSE TECHNOLOGIES, INC.

By: /s/A. Brian Davis

A. Brian Davis

Senior Vice President and Chief Financial

Officer

GEORGE J. VERGIS, PH.D.

2

/s/ George J. VergisExhibit I

Mutual Release and Non-Disparagement Agreement

THIS MUTUAL RELEASE AND NON-DISPARAGEMENT AGREEMENT (this “Mutual Release”) is made as
of the      day of      ,      by and between GEORGE VERGIS (“Executive”) and NEOSE
TECHNOLOGIES, INC. (the “Company”).

WHEREAS, Executive’s employment with the Company has ceased; and

WHEREAS, Executive has resigned as an officer and/or director of the Company and each of its
subsidiaries and affiliates; and

WHEREAS, pursuant to Section[s] 4[[,] [and] 6 [and 7]] of the Employment Agreement by and
between the Company and Executive dated February      , 2006 and effective as of May 4, 2006 (the
“Employment Agreement”), the Company has agreed to pay Executive certain amounts and to
provide him with certain rights and benefits, subject to the execution of this Mutual Release.

NOW THEREFORE, in consideration of these premises and the mutual promises contained herein,
and intending to be legally bound hereby, the parties agree as follows:

SECTION 1. Consideration. Executive acknowledges that: (i) the payments, rights and
benefits set forth in Section[s] 4[[,] [and] 6 [and 7]] of the Employment Agreement constitute full
settlement of all his rights under the Employment Agreement, (ii) he has no entitlement under any
other severance or similar arrangement maintained by the Company, and (iii) except as otherwise
provided specifically in this Mutual Release, the Company does not and will not have any other
liability or obligation to Executive. Executive further acknowledges that, in the absence of his
execution of this Mutual Release, the benefits and payments specified in Section[s] 4[[,] [and] 6
[and 7]] of the Employment Agreement would not otherwise be due to Executive.

SECTION 2. Mutual Release and Covenant Not to Sue.

2.1. The Company (including for purposes of this Section 2.1, its parents, affiliates and
subsidiaries) hereby fully and forever releases and discharges Executive (and his heirs, executors
and administrators), and Executive hereby fully and forever releases and discharges Company
(including all predecessors and successors, assigns, officers, directors, trustees, employees,
agents and attorneys, past and present) from any and all claims, demands, liens, agreements,
contracts, covenants, actions, suits, causes of action, obligations, controversies, debts, costs,
expenses, damages, judgments, orders and liabilities, of whatever kind or nature, direct or
indirect, in law, equity or otherwise, whether known or unknown, arising through the date of this
Mutual Release, out of Executive’s employment by the Company or the termination thereof, including,
but not limited to, any claims for relief or causes of action under the Age Discrimination in
Employment Act, 29 U.S.C. § 621 et seq., or any other federal, state or local statute, ordinance or
regulation regarding discrimination in employment and any claims, demands or actions based upon
alleged wrongful or retaliatory discharge or breach of contract under any state or federal law.

2.2. Executive expressly represents that he has not filed a lawsuit or initiated any other
administrative proceeding against the Company (including for purposes of this Section 2.2, its
parents, affiliates and subsidiaries) and that he has not assigned any claim against the Company or
any affiliate to any other person or entity. The Company expressly represents that it has not
filed a lawsuit or initiated any other administrative proceeding against Executive and that it has
not assigned any claim against Executive to any other person or entity. Both Executive and the
Company further promise not to initiate a lawsuit or to bring any other claim against the other
arising out of or in any way related to Executive’s employment by the Company or the termination of
that employment. This Mutual Release will not prevent Executive from filing a charge with the
Equal Employment Opportunity Commission (or similar state agency) or participating in any
investigation conducted by the Equal Employment Opportunity Commission (or similar state agency);
provided, however, that any claims by Executive for personal relief in connection with such a
charge or investigation (such as reinstatement or monetary damages) would be barred.

2.3. The foregoing will not be deemed to release the Executive or the Company from (a) claims
solely to enforce this Mutual Release, (b) claims solely to enforce Sections 4, 5, [6], [7] or 9 of
the Employment Agreement, or (c) claims solely to enforce the terms of any equity incentive award
agreement between Executive and the Company, or (d) claims for indemnification under the Company’s
By-Laws, under any indemnification agreement between the Company and Executive or under any similar
agreement.

SECTION 3. Restrictive Covenants. Executive acknowledges that restrictive covenants
contained in Section 5 of the Employment Agreement will survive the termination of his employment.
Executive affirms that those restrictive covenants are reasonable and necessary to protect the
legitimate interests of the Company, that he received adequate consideration in exchange for
agreeing to those restrictions and that he will abide by those restrictions.

SECTION 4. Non-Disparagement. The Company (meaning, solely for this purpose, the Company’s
directors and executive officers and other individuals authorized to make official communications
on the Company’s behalf) will not disparage Executive or Executive’s performance or otherwise take
any action which could reasonably be expected to adversely affect Executive’s personal or
professional reputation. Similarly, Executive will not disparage the Company or any of its
directors, officers, agents or employees or otherwise take any action which could reasonably be
expected to adversely affect the reputation of the Company or the personal or professional
reputation of any of the Company’s directors, officers, agents or employees.

SECTION 5. Cooperation. Executive further agrees that, subject to reimbursement of his
reasonable expenses, he or she will cooperate fully with the Company and its counsel with respect
to any matter (including litigation, investigations, or governmental proceedings) which relates to
matters with which Executive was involved during his employment with the Company. Executive shall
render such cooperation in a timely manner on reasonable notice from the Company.

SECTION 6. Rescission Right. Executive expressly acknowledges and recites that (a) he has
read and understands the terms of this Mutual Release in its entirety, (b) he has entered into this
Mutual Release knowingly and voluntarily, without any duress or coercion; (c) he has been advised
orally and is hereby advised in writing to consult with an attorney with respect to this Mutual
Release before signing it; (d) he was provided twenty-one (21) calendar days after receipt of the
Mutual Release to consider its terms before signing it; and (e) he or she is provided seven (7)
calendar days from the date of signing to terminate and revoke this Mutual Release, in which case
this Mutual Release shall be unenforceable, null and void. Executive may revoke this Mutual
Release during those seven (7) days by hand delivering written notice of revocation to the Company
at the address specified in Section 9.7 of the Employment Agreement.

SECTION 7. Challenge. If Executive violates or challenges the enforceability of any
provisions of the Restrictive Covenants or this Mutual Release, no further payments, rights or
benefits under Section[s] [4.2[[,] [and] 6 [and 7]] of the Employment Agreement will be due to
Executive.

SECTION 8. Miscellaneous.

8.1 No Admission of Liability. This Mutual Release is not to be construed as an
admission of any violation of any federal, state or local statute, ordinance or regulation or of
any duty owed by the Company to Executive. There have been no such violations, and the Company
specifically denies any such violations.

8.2 No Reinstatement. Executive agrees that he or she will not apply for
reinstatement with the Company or seek in any way to be reinstated, re-employed or hired by the
Company in the future.

8.3 Successors and Assigns. This Mutual Release shall inure to the benefit of and be
binding upon the Company and Executive and their respective successors, executors, administrators
and heirs. Executive not may make any assignment of this Mutual Release or any interest herein, by
operation of law or otherwise. The Company may assign this Mutual Release to any successor to all
or substantially all of its assets and business by means of liquidation, dissolution, merger,
consolidation, transfer of assets, or otherwise.

8.4 Severability. Whenever possible, each provision of this Mutual Release will be
interpreted in such manner as to be effective and valid under applicable law. However, if any
provision of this Mutual Release is held to be invalid, illegal or unenforceable in any respect,
such invalidity, illegality or unenforceability will not affect any other provision, and this
Mutual Release will be reformed, construed and enforced as though the invalid, illegal or
unenforceable provision had never been herein contained.

8.5 Entire Agreement; Amendments. Except as otherwise provided herein, this Mutual
Release contains the entire agreement and understanding of the parties hereto relating to the
subject matter hereof, and merges and supersedes all prior and contemporaneous discussions,
agreements and understandings of every nature relating subject matter hereof. This Mutual Release
may not be changed or modified, except by an Agreement in writing signed by each of the parties
hereto.

8.6 Governing Law. This Mutual Release shall be governed by, and enforced in
accordance with, the laws of the Commonwealth of Pennsylvania without regard to the application of
the principles of conflicts of laws.

8.7 Counterparts and Facsimiles. This Mutual Release may be executed, including
execution by facsimile signature, in multiple counterparts, each of which shall be deemed an
original, and all of which together shall be deemed to be one and the same instrument.

[This space left blank intentionally; signature page follows.]

3

IN WITNESS WHEREOF, the Company has caused this Mutual Release to be executed by its duly
authorized officer, and Executive has executed this Mutual Release, in each case as of the date
first above written.

NEOSE TECHNOLOGIES, INC.

By:

Name & Title:

GEORGE VERGIS

4EX-4.1

Supplemental Agreement

between

The Royal Bank of Scotland plc acting as agent for National Westminster Bank Plc

and

Sytner Group Limited

Our ref: 61076/CCD/SA

1

THIS IS AN IMPORTANT DOCUMENT. YOU SHOULD TAKE INDEPENDENT LEGAL ADVICE BEFORE SIGNING AND SIGN
ONLY IF YOU WANT TO BE LEGALLY BOUND.

THIS SUPPLEMENTAL AGREEMENT is made between:-

	(1)	 	The Royal Bank of Scotland plc (“RBS”) acting as agent for National Westminster Bank Plc; and

	(2)	 	Sytner Group Limited (the “Borrower").

WHEREAS

	(A)	 	An agreement was entered into between RBS acting as agent for National Westminster Bank Plc
and the Borrower dated 28 February 2003, amended by way of a supplemental agreement dated 25
May 2004 (together the “Agreement") setting out the terms and conditions upon and subject to
which National Westminster Bank Plc (the “Bank") agreed to make available to the Borrower a
revolving credit facility of £55,000,000 (the “Facility"); and

	(B)	 	It has been agreed between the Borrower and RBS acting as agent for National Westminster Bank
Plc that the term of the Facility shall be extended.

NOW THEREFORE IT IS AGREED:-

	1.	 	All words and expressions defined in the Agreement unless the context otherwise requires,
shall have the same meanings in this Supplemental Agreement.

	2.	 	The terms and conditions of this Supplemental Agreement shall not come into effect unless the
following conditions are satisfied:-

	(a)	 	the Bank has received and is satisfied with the duplicate of this Supplemental Agreement
signed on behalf of the Borrower; and

	(b)	 	the Bank has received and is satisfied with a certified copy of the Resolution of the Board
of Directors of the Borrower approving the transaction contemplated by this Supplemental
Agreement and authorising a specified person to sign this Supplemental Agreement on behalf of
the Borrower.

	3.	 	To reflect the change referred to in Recital (B) above the terms of the Agreement are hereby
amended as follows:-

The definition of “Final Maturity Date” in Clause 1.1 of the Agreement is hereby deleted and
replaced with the following:-

“Final Maturity Date” means 31 March 2008;

	4.	 	All other terms and conditions of the Agreement remain unaltered and shall continue in full
force and effect.

	5.	 	This Supplemental Agreement and the Agreement shall, as from the date of this Supplemental
Agreement be read and construed together as constituting the agreement between RBS acting as
agent for the Bank and the Borrower.

	6.	 	The Borrower shall pay to the Bank within 5 Business Days following the execution of this
Supplemental Agreement a fee of £25,000 in consideration of the changes contemplated by this
Supplemental Agreement.

In Witness whereof this Supplemental Agreement is executed by the duly authorised representatives
of the Bank and the Borrower.

For and on behalf of RBS acting as agent for the Bank

/s/ Andrew Baker

Signature

Date May 8, 2006

For and on behalf of the Borrower

/s/ Mark Carpenter

Signature

Date May 8, 2006

2

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