Document:

EX-10.3

Exhibit 10.3

Order No.

Escrow No.

Loan No.

WHEN RECORDED MAIL TO:

Joe Prudente

41 Main Street

Bolton Mass 01740

SPACE ABOVE THIS LINE FOR RECORDER’S USE

DEED OF TRUST WITH ASSIGNMENT OF RENTS

(LONG FORM)

(ACCELERATION CLAUSE)

This DEED OF TRUST, made as of January 19, 2006, between SIPEX CORPORATION, a Delaware corporation,
herein called TRUSTOR, whose address is 233 South Hillview Drive, Milpitas, CA 95035, Attention:
Chief Financial Officer, FIRST AMERICAN TITLE INSURANCE COMPANY, a California corporation, herein
called TRUSTEE, and RODFRE HOLDINGS LLC, a Delaware limited liability company, herein called
BENEFICIARY

WITNESSETH: That Trustor grants to Trustee in Trust, with Power of Sale, that property (the
“Property”) in the City of Milpitas, County of Santa Clara, State of California, described as:

SEE EXHIBIT “A” ATTACHED HERETO AND MADE A PART HEREOF

together with the rents, issues and profits thereof, subject, however, to the right, power and
authority hereinafter given to and conferred upon Beneficiary to collect and apply such rents,
issues and profits for the Purpose of Securing (1) payment of the sum of U.S. $7,000,000, with
interest thereon according to the terms of that certain 9% Secured Note with Convertible Interest
Due January 19, 2008 (the “Note”) of even date herewith made by Trustor, payable to order of
Beneficiary, and extensions or renewals thereof, (2) the performance of each agreement of Trustor
incorporated by reference or contained herein and (3) payment of additional sums and interest
thereon which may hereafter be loaned to Trustor, or its successors or assigns, by Beneficiary when
evidenced by a promissory note or notes reciting that they are secured by this Deed of Trust;
provided, however, that in no event shall the aggregate indebtedness secured by this Deed of Trust
at any time exceed the sum of the outstanding principal amount of the Note, plus all accrued and
unpaid interest thereon, plus U.S. $1,400,000.

Notwithstanding anything in this Deed of Trust to the contrary, in no event shall the Property
include any personal property or equipment owned or leased by Trustor, whether or not located on
the Property or used in connection therewith. However, to the extent that the same may be
considered as being, or having become part of the buildings and without any admission to that
effect on the part of the Trustor, Trustor’s specialized systems (including, without limitation
“clean-room” facilities) currently existing, or hereafter incorporated from time to time, into the
buildings located on the Property, shall be included within the scope of this Deed of Trust, and
shall be considered to form part of the Property.

If Trustor shall sell, convey, or alienate the Property, or any part thereof, or any interest
therein, or shall be divested of its title or any interest therein in any manner or way, whether
voluntarily or involuntarily, without the written consent of the Beneficiary being first had and
obtained, Beneficiary shall have the right, at its option, except as prohibited by law, to declare
any indebtedness or obligations secured hereby, irrespective of the maturity date specified in any
note evidencing same, immediately due and payable.

A. To protect the security of this Deed of Trust, Trustor agrees:

(1) To keep the Property in good condition and repair; not to remove or demolish any building
thereon; to complete or restore promptly and in good and workmanlike manner any building which may
be constructed, damaged or destroyed thereon, provided that Beneficiary makes available to Trustor
the proceeds of any insurance received on account of such damage or destruction, and to pay when
due all claims for labor performed and materials furnished therefor; to comply with all laws
affecting the Property or requiring any alterations or improvements to be made thereon; to comply
with all recorded instruments relating to the maintenance or use of the Property; not to commit or
permit waste thereof; not to commit, suffer or permit any act upon the Property in violation of
law; to do all other acts which from the character or use of the Property may be reasonably
necessary to preserve the value thereof, the specific enumerations herein not excluding the
general. Notwithstanding anything to the contrary in this Deed of Trust, no failure to comply with
any such laws or recorded instruments or to do any such acts shall constitute a default of Trustor
unless it could reasonably be expected to have a Material Adverse Effect, which, for the purposes
of this Deed of Trust, shall be deemed to occur if the cost to remedy the failure or non-compliance
or the likely reduction in the fair market value of the Property as a result of the failure or
non-compliance, which ever is greater, exceeds $600,000. The determination of the fair market
value of the Property and its likely reduction shall be made by Stan Tish of Berliner, Kidder &
Tish, 480 Lytton Avenue, Suite 2, Palo Alto, CA 94301, or such other appraiser as shall be approved
by Trustor and Beneficiary who is a Member of the Appraisal Institute and has experience in valuing
commercial and industrial properties in Santa Clara County. In the event the appraiser determines
that there is a Material Adverse Effect, the cost of the appraisal shall be borne by Trustor;
otherwise, the cost of the appraisal shall be borne by Beneficiary. Notwithstanding the foregoing,
Trustor may modify the “clean room” facilities currently existing, or hereafter incorporated from
time to time, into the buildings located on the Property, to alter or improve such “clean room”
facilities in the ordinary course of Trustor’s business.

(2) To provide, maintain and deliver to Beneficiary property insurance reasonably satisfactory
to and with loss payable to Beneficiary. Without limiting the generality of the foregoing,
Beneficiary shall have the right to reasonably approve the nature and scope of the property
insurance coverage, the identity of the insurer(s), the amount of insurance coverage and the amount
of any deductibles or self-insured retention and to require that Trustor forthwith subscribe, and
maintain in effect, such additional or different insurance coverage as Beneficiary, acting
reasonably, may deem appropriate or desirable. Within thirty (30) days after the date hereof, the
Trustor shall provide the Beneficiary with a certificate and summary of all property, business
interruption, liability, workmen’s compensation and other insurance subscribed by the Trustor. All
amounts collected under any property insurance policy shall be released to Trustor for the repair
and restoration of the Property pursuant to a disbursement procedure reasonably acceptable to
Beneficiary, provided that if, with Beneficiary’s consent, the Property is not to be so repaired or
restored, all amounts so collected shall be applied by Beneficiary upon the indebtedness secured
hereby. Such release or application shall not cure or waive any default or notice of default
hereunder or invalidate any act done pursuant to such notice.

(3) To appear in and defend any action or proceeding purporting to affect the security hereof
or the rights or powers of Beneficiary or Trustee; and to pay all costs and expenses, including
cost of evidence of title and attorney’s fees in a reasonable sum, in any such action or proceeding
in which Beneficiary or Trustee may appear, and in any suit brought by Beneficiary to foreclose
this Deed of Trust.

(4) To pay: at least ten days before delinquency all taxes and assessments affecting the
Property, including assessments on appurtenant water stock; when due, all encumbrances, charges and
liens, with interest, on the Property or any part thereof, which appear to be prior or superior
hereto; all costs, fees and expenses of this Trust.

Should Trustor be in default under this Deed of Trust, beyond applicable notice and cure
periods, due to Trustor’s failure to make any payment or to do any act as herein provided, then
Beneficiary or Trustee, but without obligation so to do but with prior notice to Trustor and
without releasing Trustor from any obligation hereof, may: make or do the same in such manner and
to such extent as either may reasonably deem necessary to protect the security hereof, Beneficiary
or Trustee being authorized to enter upon the Property for such purposes; appear in and defend any
action or proceeding purporting to affect the security hereof or the rights or powers of
Beneficiary or Trustee; pay, purchase, contest or compromise any encumbrance, charge or lien which
in the judgment of either appears to be prior or superior hereto; and, in exercising any such
powers, pay necessary expenses, employ counsel and pay his reasonable fees.

(5) To pay immediately and without demand all sums so expended by Beneficiary or Trustee, with
interest from date of expenditure at the amount allowed by law in effect at the date hereof, and to
pay for any statement provided for by law in effect at the date hereof regarding the obligation
secured hereby any amount demanded by the Beneficiary not to exceed the maximum allowed by law at
the time when said statement is demanded.

(6) To comply with the following provisions concerning environmental laws and hazardous
substances, failure with which to comply could reasonably be expected to have a Material Adverse
Effect.

(a) As used in this paragraph 6:

(i) “Environmental Laws” shall mean all federal, state and local laws, ordinances, rules and
regulations now or hereafter in force, as amended from time to time, in any way relating to or
regulating human health or safety, industrial hygiene or protection of the environment.

(ii) “Hazardous Substances” shall mean any substance or material that is described,
designated or regulated as a toxic or hazardous substance, waste or material or a pollutant or
contaminant, or words of similar import, in any of the Environmental Laws.

(iii) “Release” shall mean any spilling, leaking, pumping, pouring, emitting, emptying,
discharging, injecting, escaping, leaching, dumping or disposing into the environment, including
continuing migration, of Hazardous Substances into, onto or through the soil, surface water or
groundwater of the Property, whether or not caused by, contributed to, permitted by, acquiesced to
or known to Trustor in violation of Environmental Laws.

(iv) “User” means any person other than Trustor who occupies, uses or comes onto or has
occupied, used or come onto the Property or any part thereof and any agent or contractor of such a
person.

(b) Trustor represents and warrants to Beneficiary that as of the date of this Deed of Trust
and to the best of Trustor’s knowledge, based on due inquiry and investigation (which inquiry and
investigation, as to any property other than the Property, is based on and limited to environmental
assessments prepared by Trustor’s consultants):

(i) except as previously disclosed in writing by Trustor to Beneficiary (A) no Hazardous
Substances in excess of permitted levels or reportable quantities under applicable Environmental
Laws are present in, on or under the Property or any nearby real property which could migrate to
the Property, (B) no Release or threatened Release exists or has occurred, (C) neither Trustor nor
any User has ever used the Property or any part thereof for the production, manufacture,
generation, treatment, handling, storage, transportation or disposal of Hazardous Substances in
violation of Environmental Laws, (D) no underground, surface or elevated storage tanks of any kind,
wells (except domestic water wells), septic tanks, pits, ponds or other impoundments (“Tanks”) are
or ever have been located in or on the Property, and (E) no investigation, claim, demand, action or
proceeding of any kind relating to any Release or threatened Release or any past or present
violation of any Environmental Laws relating to the Property has been made or commenced, or is
pending, or is being threatened by any governmental authority or other person;

(ii) all operations and activities at, and the use and occupancy of, the Property comply with
all applicable Environmental Laws to the extent that non-compliance with any of the foregoing could
reasonably be expected to have a Material Adverse Effect;

(iii) Trustor is in strict compliance with, and Trustor has not received any notice that any
User is not in compliance with, every permit, license and approval required by all applicable
Environmental Laws for all activities and operations at, and the use and occupancy of, the
Property, to the extent that non-compliance with any of the foregoing could reasonably be expected
to have a Material Adverse Effect;

(iv) neither the Property, nor any portion thereof, nor any adjacent property or portion
thereof, has been or is proposed to be listed under the Comprehensive Environmental Response,
Compensation and Liability Act (42 U.S.C. Section 9601, et seq.), or any analogous state law; and

(v) any written disclosure submitted by or on behalf of Trustor to Beneficiary at
Beneficiary’s request concerning any Release or threatened Release, past or present compliance by
Trustor, User or any other person of any Environmental Laws applicable to the Property, the past
and present use and occupancy of the Property, any environmental concerns relating to the Property
and the like, was true and complete when submitted to the extent that any inaccuracy or
incompleteness of the disclosure could reasonably be expected to have a Material Adverse Effect.

(c) Trustor agrees that:

(i) Except in the ordinary course of business, and in compliance with all applicable
Environmental Laws, Trustor promises that neither Trustor nor any User shall use, produce,
manufacture, generate, treat, handle, store, transport, or dispose of any Hazardous Substances in,
on or under the Property, or use the Property for any such purposes in such a manner as could
reasonably be expected to have a Material Adverse Effect;

(ii) Trustor shall not cause, contribute to, permit or acquiesce to any Release or threatened
Release;

(iii) Trustor shall comply fully, and shall cause every User to comply fully, with all
Environmental Laws applicable to the Property, and all other laws, ordinances and regulations
applicable to the use or occupancy thereof, or any operations or activities therein or thereon, to
the extent that non-compliance with any of the foregoing could reasonably be expected to have a
Material Adverse Effect;

(iv) With respect to any Tanks disclosed in writing to Beneficiary, Trustor shall comply with
all Environmental Laws and any requirements of city or county fire departments, applicable to the
maintenance and use of such Tanks, including, without limitation, Title 40 of the Code of Federal
Regulations part 112, the non-compliance with which could reasonably be expected to have a Material
Adverse Effect;

(v) To facilitate performance of Trustor’s obligations under subparagraphs (c)(i), (ii),
(iii) and (iv) of this paragraph A (6)(c), Trustor shall regularly inspect the Property, monitor
the activities and operations of every User and confirm that every User has obtained and fully
complies with all permits, licenses and approvals required by all applicable Environmental Laws,
the non-compliance with which could reasonably be expected to have a Material Adverse Effect;

(vi) Promptly after Trustor obtains any information indicating any Release or threatened
Release, or that Hazardous Substances in, on or under any nearby property could migrate to the
Property or a violation of any Environmental Laws may have occurred or could occur regarding the
Property, Trustor shall give notice thereof to Beneficiary with a reasonably detailed description
of the event, occurrence or condition in question;

(vii) If Beneficiary obtains any information that Beneficiary believes in good faith
indicates a reasonable possibility of a Release or threatened Release, or that Hazardous Substances
in, on or under any nearby real property could migrate to the Property or any violation of any
Environmental Laws may have occurred or could occur regarding the Property, then Trustor shall, at
the expense of Trustor, promptly after a request by Beneficiary, or Beneficiary may at Trustor’s
expense any time prior to completion of a judicial or nonjudicial foreclosure, engage a qualified
environmental engineer to conduct a comprehensive environmental assessment of the Property and
prepare and submit to Beneficiary a written report containing the findings and conclusions
resulting from such investigation. Trustor shall, on demand, pay to Beneficiary all sums expended
by Beneficiary in connection with any such comprehensive environmental assessment;

(viii) Trustor shall permit, or cause any User to permit, Beneficiary or its agents or
independent contractors to enter and inspect the Property (including the taking of building
materials, soil and groundwater samples) at any reasonable time and after reasonable notice, except
in an emergency, whether or not a default has occurred under this Deed of Trust, and including
after the commencement of judicial or nonjudicial foreclosure proceedings, for purposes of
determining, to the extent reasonably necessary, the existence, location or nature of any Hazardous
Substances into, onto, or spread beneath or from the Property, that is located or has been spilled,
disposed of, discharged or released on, under or about the Property. Trustor acknowledges that all
inspections and reviews undertaken by Beneficiary are solely for the benefit and protection of
Beneficiary and agrees that Beneficiary shall have no duty to Trustor with respect to Hazardous
Substances or Environmental Laws as a result of any such inspections, and such inspections shall
not result in a waiver of any default by Trustor. If Trustor or any User fails to comply fully with
the terms of this provision, Beneficiary may obtain affirmative injunctive relief to compel such
compliance; and

(ix) If any Release or threatened Release exists or occurs before this Deed of Trust is
reconveyed or foreclosed upon, or if Trustor is in breach of any of its representations, warranties
or covenants as set forth in this paragraph A (6), Trustor shall promptly give notice of the
condition to Beneficiary, and Trustor shall at its own expense cause all Hazardous Substances to be
cleaned up and removed from the Property, and the Property shall be restored, in compliance with
all applicable Environmental Laws and other laws, ordinances, rules and regulations (the
“Remediation Work”). If requested by Beneficiary, Trustor shall submit to Beneficiary, for
Beneficiary’s prior approval, complete plans and specifications for all Remediation Work to be done
before any Remediation Work is performed, except in an emergency. Alternatively, if Trustor is in
default hereunder beyond applicable notice and cure periods, Beneficiary may cause such Remediation
Work to be completed at Trustor’s expense.

(d) Beneficiary shall have the right to advise appropriate governmental authorities of any
environmental condition on or affecting the Property to the extent that Beneficiary is obligated to
do so under applicable law.

(e) Trustor and its successors and assigns shall indemnify, defend, protect, and hold
harmless Beneficiary, and/or Trustee, its directors, officers, employees, agents, shareholders,
successors and assigns and their officers, employees or agents, from and against any and all
claims, suits, damages, foreseeable and unforeseeable consequential damages, liens, losses,
liabilities, interest, judgments, cleanup costs, demands, actions, causes of action, injuries,
administrative proceedings and orders, consent agreements and orders, penalties, costs and expenses
(including any fees and expenses incurred in enforcing this indemnity, any reasonable out-of-pocket
litigation costs, sums paid in settlement of claims, and all reasonable consultant, expert and
counsel fees and expenses, including in-house legal services) of any kind whatsoever (“Claims”)
paid, incurred or suffered by, or asserted against Beneficiary and/or Trustee, including but not
limited to Claims arising out of loss of life, injury to persons, trespass or damage to or
contamination of property or natural resources, or injury to business, in connection with or
arising out of the activities of Trustor on the Property, Trustor’s predecessors in interest, third
parties who have been invited, permitted or trespassed on the Property, or parties in a contractual
relationship with Trustor, or any of them, or which directly or indirectly arise out of or result
from or in any way connected with the Property, whether or not caused by Trustor or within the
control of Trustor, including without limitation: (i) the Release, threatened Release of any
Hazardous Material at, from, within, on or under the Property; (ii) Trustor’s breach of any of the
representations, warranties and covenants contained herein; and (iii) Trustor’s violation or
alleged violation of any applicable Environmental Law. The foregoing indemnity shall not include
any Claims to the extent attributable to the actions or failure to act of Beneficiary or any
persons for whom Beneficiary is legally responsible.

(f) Trustor’s representations, warranties, covenants and indemnities contained herein shall
survive the occurrence of any event whatsoever, including without limitation the payoff of the
promissory note secured hereby, the reconveyance or foreclosure of this Deed of Trust, the
acceptance by Trustee of a deed in lieu of foreclosure, or any transfer or abandonment of the
Property.

B. It is mutually agreed:

(1) That any award of damages in connection with any condemnation for public use of or injury
to said property or any part thereof is hereby assigned and shall be paid to Beneficiary who shall
apply or release such moneys received by it in the same manner and with the same effect as above
provided for disposition of proceeds of fire or other insurance.

(2) That by accepting payment of any sum secured hereby after its due date, Beneficiary does
not waive its right to require prompt payment when due of all other sums so secured.

(3) That at any time or from time to time, without liability therefor and without notice, upon
written request of Beneficiary and presentation of this Deed of Trust and said note for
endorsement, and without affecting the personal liability of any person for payment of the
indebtedness secured hereby, Trustee may: reconvey any part of the Property; consent to the making
of any map or plat thereof; join in granting any easement thereon; or join in any extension
agreement or any agreement subordinating the lien or charge hereof.

(4) That upon written request of Beneficiary stating that all sums secured hereby have been
paid or otherwise satisfied, and upon surrender of this Deed of Trust and said note to Trustee for
cancellation and retention or other disposition as Trustee in its sole discretion may choose and
upon payment of its fees, Trustee shall reconvey, without warranty, the property then held
hereunder. The recitals in such reconveyance of any matters or facts shall be conclusive proof of
the truthfulness thereof. The Grantee in such reconveyance may be described as “the person or
persons legally entitled thereto.”

(5) That as additional security, Trustor hereby gives to and confers upon Beneficiary the
right, power and authority, during the continuance of these Trusts, to collect the rents, issues
and profits of said property, reserving unto Trustor the right, prior to any default by Trustor in
payment of any indebtedness secured hereby or in performance of any agreement hereunder, to collect
and retain such rents, issues and profits as they become due and payable. Upon any such default,
Beneficiary may at any time by a receiver to be appointed by a court, and without regard to the
adequacy of any security for the indebtedness hereby secured, enter upon and take possession of the
Property or any part thereof, in its own name sue for or otherwise collect such rents, issues, and
profits, including those past due and unpaid, and apply the same, less costs and expenses of
operation and collection, including reasonable attorney’s fees, upon any indebtedness secured
hereby, and in such order as Beneficiary may determine. The entering upon and taking possession of
the Property, the collection of such rents, issues and profits and the application thereof as
aforesaid, shall not cure or waive any default or notice of default hereunder or invalidate any act
done pursuant to such notice.

(6) That upon default by Trustor in payment of any indebtedness secured hereby or in
performance of any agreement hereunder, Beneficiary may declare all sums secured hereby immediately
due and payable by delivery to Trustee of written declaration of default and demand for sale and of
written notice of default and of election to cause to be sold said property, which notice Trustee
shall cause to be filed for record. Beneficiary also shall deposit with Trustee this Deed of
Trust, said note and all documents evidencing expenditures secured hereby.

After the lapse of such time as may then be required by law following the recordation of said
notice of default, and notice of sale having been given as then required by law, Trustee, without
demand on Trustor, shall sell the Property at the time and place fixed by it in said notice of
sale, either as a whole or in separate parcels, and in such order as it may determine, at public
auction to the highest bidder for cash in lawful money of the United States, payable at time of
sale. Trustee may postpone sale of all or any portion of the Property by public announcement at
such time and place of sale, and from time to time thereafter may postpone such sale by public
announcement at the time fixed by the preceding postponement. Trustee shall deliver to such
purchaser its deed conveying the Property so sold, but without any covenant or warranty, express or
implied. The recitals in such deed of any matters or facts shall be conclusive proof of the
truthfulness thereof. Any person, including Trustor, Trustee, or Beneficiary as hereinafter
defined, may purchase at such sale.

After deducting all costs, fees and expenses of Trustee and of this Trust, including cost of
evidence of title in connection with sale, Trustee shall apply the proceeds of sale to payment of:
all sums expended under the terms hereof, not then repaid, with accrued interest at the amount
allowed by law in effect at the date hereof; all other sums then secured hereby; and the remainder,
if any, to the person or persons legally entitled thereto.

Notwithstanding anything to the contrary in the Note, this Deed of Trust, or any other
document or instrument evidencing or securing the indebtedness evidenced by the Note, no failure of
Trustor to pay, observe or perform any term or condition thereof, and no inaccuracy of any
representation or warranty thereunder, shall constitute a default of Trustor until Beneficiary has
delivered Trustor written notice thereof and Trustor has failed to cure the same (i) within ten
(10) days thereafter as regards matters that may be cured solely by the payment of money, or (ii)
within thirty (30) days thereafter as regards all other matters, provided, however, that if such
matter cannot reasonably be cured within thirty (30) days, as long as Trustor promptly commences
such cure and diligently proceeds with such cure, such period shall be extended for the reasonable
time required to perform such cure.

(7) Beneficiary, or any successor in ownership of any indebtedness secured hereby, may from
time to time, by instrument in writing, substitute a successor or successors to any Trustee named
herein or acting hereunder, which instrument, executed by the Beneficiary and duly acknowledged and
recorded in the office of the recorder of the county or counties where the Property is situated,
shall be conclusive proof of proper substitution of such successor Trustee or Trustees, who shall,
without conveyance from the Trustee predecessor, succeed to all its title, estate, rights, powers
and duties. Said instrument must contain the name of the original Trustor, Trustee and Beneficiary
hereunder, the book and page where this Deed of Trust is recorded and the name and address of the
new Trustee.

(8) That this Deed of Trust applies to, inures to the benefit of, and binds all parties
hereto, their heirs, legatees, devisees, administrators, executors, successors and assigns. The
term Beneficiary shall mean the owner and holder, including pledgees of the note secured hereby,
whether or not named as Beneficiary herein. In this Deed of Trust, whenever the context so
requires, the masculine gender includes the feminine and/or neuter, and the singular number
includes the plural.

(9) That Trustee accepts this Trust when this Deed of Trust, duly executed and acknowledged,
is made a public record as provided by law. Trustee is not obligated to notify any party hereto of
pending sale under any other Deed of Trust or of any action or proceeding in which Trustor,
Beneficiary or Trustee shall be a party unless brought by Trustee.

The undersigned Trustor, requests that a copy of any notice of default and any notice of sale
hereunder be mailed to it at its address hereinbefore set forth.

	 
	 

	Signature of Trustor

	 

	SIPEX CORPORATION

	 

	By: /s/ Clyde R. Wallin     

	 
	 	 	Its Sr. VP Finance & CFO

	 	 	 
	STATE OF CALIFORNIA

	 	}

}ss.

COUNTY OF Santa Clara}

On January 17, 2006 before me, Judy Coulter  , personally appeared  Clyde
R. Wallin , personally known to me (or proved to me on the basis of satisfactory evidence) to
be the person whose name is subscribed to the within instrument and acknowledged to me that he
executed the same in his authorized capacity, and that by his signature on the instrument the
person or the entity upon behalf of which the person acted, executed the instrument.

WITNESS my hand and official seal.

Signature /s/ Judy Coulter

1

	 	 	 
	(This area for official notarial seal)
	DO NOT RECORD	 	REQUEST FOR FULL RECONVEYANCE

TO FIRST AMERICAN TITLE INSURANCE COMPANY, TRUSTEE:

The undersigned is the legal owner and holder of the note or notes, and of all other indebtedness
secured by the foregoing Deed of Trust. Said note or notes, together with all other indebtedness
secured by said Deed of Trust, have been fully paid and satisfied; and you are hereby requested and
directed, on payment to you of any sums owing to you under the terms of said Deed of Trust, to
cancel said note or notes above mentioned, and all other evidences of indebtedness secured by said
Deed of Trust delivered to you herewith, together with the said Deed of Trust, and to reconvey,
without warranty, to the parties designated by the terms of said Deed of Trust, all the estate now
held by you under the same.

Dated

Please mail Deed of Trust,

Note and Reconveyance to     

Do not lose or destroy this Deed of Trust OR THE NOTE which it secures. Both must be delivered to
the Trustee for cancellation before reconveyance will be made.

EXHIBIT “A”

to

DEED OF TRUST WITH ASSIGNMENT OF RENTS

Real property in the City of Milpitas, County of Santa Clara, State of California, described as
follows:

PARCEL ONE:

Parcel 2, as shown on that certain Map entitled, “Parcel Map being a portion of Parcel 3, as shown
upon that certain Parcel Map recorded in Book 493 of Maps page(s) 19 and 20, Records of Santa Clara
County,” which Map was filed for record in the office of the Recorder of the County of Santa Clara,
State of California on May 24, 1989 in Book 586 of Maps, at pages 37 and 38.

PARCEL TWO:

An easement for the purpose of ingress and egress, said easement being more particularly described
as follows:

Being a portion of Parcel 3 as shown upon that certain Parcel Map, recorded in Book 493 of maps, at
page 19 and 20, Records of Santa Clara County, being more particularly described as follows:

Commencing at a point on the Northeasterly boundary line of said Parcel 3, said point being the
Southerly terminus of the course shown as “R=75 angle = 124° 50’ 34” L=163.42” on said map.

Thence, from said point of commencement, along said Northeasterly boundary line of said Parcel 3,
from a tangent bearing of N. 41° 25’ 04” W., along a curve to the right, having a radius of 75.00
feet, through a central angle of 17° 25’ 24”, for an arc length of 22.81 feet; thence, leaving said
Northeasterly line N. 23° 59’40” W. 75.00 feet; thence S. 66° 00’ 20” W., 21.77 feet; thence, N.
23° 59’40” W., 214.85 feet to the true point of beginning; thence, from said true point of
beginning S. 66° 00’ 20” W., 116.50 feet; thence N. 23° 59’ 40” W., 12.50 feet; thence N. 66° 00’
20” E. 116.50 feet; thence, S. 23° 59’ 40” E., 12.50 feet to the true point of beginning.

PARCEL THREE:

An easement for the purpose of a Private Sanitary Sewer and Private Storm Drainage, said easement
being more particularly described as follows:

Being a portion of Parcel 3 as shown upon that certain Parcel Map recorded in Book 493 of Maps, at
pages 19 and 20, Records of Santa Clara County, being more particularly described as follows:

Commencing at a point in a Northeasterly boundary line of said Parcel 3 said point being the
Southerly terminus of the course shown as “R=75, angle = 124° 50’34”, L=163.42” on said Map.

Thence, from said point of commencement, along said Northeasterly boundary line of said Parcel 3,
from a tangent bearing of N. 41° 25’ 04” W, along a curve to the right, having a radius of 75.00
feet, through a central angle of 17° 25’ 24”, for an arc length of 22.81 feet; thence, leaving said
Northwesterly line N. 23° 59 ‘40” W., 40.00 feet to a point in the line designated as “10’ PSUE &
PE” on said Map said point being the true point of beginning; thence, from said true point of
beginning, N. 23° 59’ 40” W. 35.000 feet; thence, N. 66° 00’ 20” E., 35.00 feet to a point in said
line designated as “10’ PSUE and PE”; thence, along said line, from a tangent bearing of S. 37° 55’
59” W., along a curve to the left, having a radius of 85.00 feet, through a central angle of 33°
51’ 18”, for an arc length of 50.22 feet to the true point of beginning.

PARCEL FOUR:

An easement for the purpose of Private Storm Drainage, said easement being more particularly
described as follows:

Being a portion of Parcel 3 as shown upon that certain Parcel Map recorded in Book 493 of Maps, at
pages 19 and 20, Records of Santa Clara County, being more particularly described as follows:

Being a strip of land uniform width of 10.00 feet, measured at right angles, the center line of
which is described as follows:

Commencing at a point in a Northeasterly boundary line of said Parcel 3 said point being the
Southerly terminus of the course shown as “R=75, angle 124° 50’34”, L = 163.42” on said Map.

Thence, from said point of commencement, along said Northeasterly boundary line of said Parcel 3,
from a tangent bearing of N 41° 25’ 04” W., along a curve to the right, having a radius of 75.00
feet, through a central angle of 17° 25’ 24”, for an arc length of 22.81 feet; thence, leaving said
Northeasterly line N. 23° 59’ 40” W. 75.00; thence, S. 66° 00’ 20” W. 21.77 feet; thence N. 23° 59’
40” W, 227.35 feet; thence, S. 66° 00’ 20” W., 116.50 feet; thence, N. 23° 59’ 40” W., 36.25 feet
to the true point of beginning; thence, from said true point of beginning S. 54° 14’ 14” W., 6.13
feet; thence, S. 72° 32’ 10” W., 231.38 feet; thence, S. 11° 55’ 04” E. 151.16 feet to a point in a
line parallel with and 6.00 feet Northeasterly, measured at right angles, from the Southwesterly
line of said Parcel 3; thence, along said parallel line S. 23° 59’ 40” E., 447.50 feet to the
intersection thereof with the adjusted lot line per City of Milpitas, Resolution N. 5318, dated
July 15, 1986; said point being the terminal point of herein described center line.

PARCEL FIVE:

An easement for the purpose of Private Sanitary Sewer and Private Storm Drainage, said easement
being more particularly described as follows:

Being a portion of parcels 2 and 3 as shown upon that certain parcel Map, recorded in Book 493 of
Maps at pages 19 and 20, Records of Santa Clara County, being more particularly described as
follows:

Commencing at the most Southerly corner of said Parcel 3; thence from said Point of Commencement,
along the Southwesterly boundary line of said Parcel 2, S 23° 59’ 40” E, 10.00 feet to the True
Point of Beginning; thence, from said True Point of Beginning, leaving said line, at right angles,
parallel with the Southeasterly boundary line of said Parcel 3, N 66° 00’ 20” E, 20.00 feet;
thence, at right angles, parallel with the aforementioned Southwesterly boundary line, N 23° 59’
40” W, 42.50 feet; thence, at right angles, parallel with the aforementioned Southeasterly boundary
line, S 66° 00’ 20” W, 20.00 feet to a point in the Southwesterly boundary line of said Parcel 3;
thence, along said Southwesterly boundary line of said Parcel 3 and Parcel 2 at right angles, S 23°
59’ 40” E, 42.50 feet to the True Point of Beginning.

APN: 086-38-029

ARB: 86-28-13.03.06

2EX-10.4

 Exhibit 10.4

AMENDMENT NO. 3

TO

LOAN AND SECURITY AGREEMENT

THIS AMENDMENT NO. 3 TO LOAN AND SECURITY AGREEMENT (this “Amendment”) is entered into this
19th day of January, 2006, by and between Silicon Valley Bank (“Bank”) and Sipex
Corporation, a Delaware corporation (“Borrower”) whose address is 233 South Hillview Drive,
Milpitas, California 95035.

Recitals

A. Bank and Borrower have entered into that certain Loan and Security Agreement dated as of
July 21, 2005 (as the same may from time to time be amended, modified, supplemented or restated,
the “Loan Agreement”).

B. Bank has extended credit to Borrower for the purposes permitted in the Loan Agreement.

C. Borrower has requested that Bank amend the Loan Agreement to make certain revisions to the
Loan Agreement as more fully set forth herein.

D. Bank has agreed to so amend certain provisions of the Loan Agreement, but only to the
extent, in accordance with the terms, subject to the conditions and in reliance upon the
representations and warranties set forth below.

Agreement

Now, Therefore, in consideration of the foregoing recitals and other good and
valuable consideration, the receipt and adequacy of which is hereby acknowledged, and intending to
be legally bound, the parties hereto agree as follows:

1. Definitions. Capitalized terms used but not defined in this Amendment shall have
the meanings given to them in the Loan Agreement.

2. Amendments to Loan Agreement.

2.1 Section 2.3 (Interest Rate). The first sentence of Section 2.3(a) is amended in
its entirety to read as follows: “Advances accrue interest on the outstanding balance at a
per annum rate equal to the Prime Rate plus two percent (2.00%).”

2.2 Section 6.10 (Real Estate Transaction). A new Section 6.10 is hereby inserted
after Section 6.9 as follows:

“6.10 Real Estate Transaction. (a) The transactions contemplated by the Real Estate
Documents (as defined below) shall be consummated on or prior to January 31, 2006 in
accordance with the terms of the Real Estate Documents, (b) all the conditions precedent
shall have been satisfied such that Borrower shall have access to or have borrowed at least
$7,000,000 pursuant to such Real Estate Documents and (c) Borrower, Rodfre Holdings LLC and
Bank shall have entered into a Subordination Agreement in the form of Exhibit A hereto (the
“Subordination Agreement”).”

2.3 Section 7.1 (Dispositions). Section 7.1 is amended in its entirety to read as
follows:

“7.1 Dispositions. Convey, sell, lease, transfer or otherwise dispose of (collectively
“Transfer”), or permit any of its Subsidiaries to Transfer, all or any part of its business
or property, except for Transfers (a) of Inventory in the ordinary course of business; (b)
of exclusive or non-exclusive licenses and similar arrangements for the use of the property
of Borrower or its Subsidiaries in the ordinary course of business; (c) of worn-out or
obsolete Inventory and Equipment; (d) permitted under Sections 7.3 or 7.6; (e) of the real
estate located at 233 South Hillview Drive, Milpitas, California (the “Property”) and as
further described in that certain Deed of Trust with Assignment of Rents dated as of January
19, 2006 (the “Deed of Trust”) among the Borrower, First American Title Insurance Company
and Rodfre Holdings LLC; provided that (1) such sale price, terms and conditions are
commercially reasonable and (2) the net proceeds received by Borrower from such sale is
equal to or greater than the entire outstanding principal amount under the 9% Secured Note
with Convertible Interest Due January 19, 2008 (the “9% Note”), together with all accrued
and unpaid interest thereon, and (f) other Transfers of property having an aggregate book
value not to exceed $500,000 in any fiscal year.”

2.4 Section 7.7 (Transactions with Affiliates). Section 7.7 is amended in its entirety
to read as follows:

“Section 7.7 Transactions with Affiliates. Directly or indirectly enter into or
permit to exist any material transaction with any Affiliate of Borrower except for (i)
transactions that are in the ordinary course of Borrower’s business, upon fair and
reasonable terms that are no less favorable to Borrower than would be obtained in an arm’s
length transaction with a nonaffiliated Person; (ii) customary fees, expenses and
compensation including employee benefits paid or reimbursed to directors, officers or
employees who are Affiliates; and (iii) transactions permitted under Section 7.4 (with
respect to the transaction described under clause (i) of the definition of Permitted
Indebtedness) or under Section 7.6.

2.5 Section 13 (Definitions). The following definition set forth in Section 13.1 is
amended as follows:

The definition of “Borrowing Base” is amended and restated in its entirety as follows:

““Borrowing Base” is, as determined by Bank from borrower’s most recent Borrowing Base
Certificate, the sum of (a) 70% of Eligible Accounts owing from Chander Electronics, Gold
InsigniaElectronic Co. LTD, Jetronic, Kohmatsu, Lestina International, LSD MCU (HK) Science
and Tech, MFS Technology, Microtek, Princeton Technology, Prohubs, Silicon Applications,
Tomuki Corporation, AMSC and Hong Kong Baite; (b) 80% of Eligible Accounts owing from Avnet
Electronics, Celestica, Dell, Flextronics International, Fuji Electronics, Future
Electronics (UK), Future Electronics (Canada), Future Electronics (Malaysia), Honeywell,
IBM, Jabil, Jaco Electronics, Paradyne Corporation, Philips, Raytheon, Sammex (Scientific
Atlanta, Mexico), Samsung, Sanmina, Toshiba, and (c) a percentage of such other Eligible
Accounts as Bank may approve in its sole discretion; provided however, that Bank may
decrease the foregoing percentages in its good faith business judgment based on events,
conditions, contingencies, or risks, which, as determined by Bank, may adversely affect the
Collateral, or in accordance with the results of the initial field exam and on-going
periodic exams.”

In the definition of “Permitted Indebtedness”, the “and” at the end of clause (g) is
hereby deleted, the “.” after clause (h) is replaced with “; and” and the following new
clause (i) shall be inserted thereafter:

“(i) Indebtedness under the 9% Note (as defined in Section 7.1).”

In the definition of “Permitted Liens”, the “and” at the end of clause (m) is hereby
deleted, the “.” after clause (n) is replaced with “; and” and the following new clause (o)
shall be inserted thereafter:

“(o) Liens in favor of Rodfre Holdings LLC on the Property to secure Borrower’s
obligations under the Deed of Trust and the 9% Note; provided however, neither the Deed of
Trust, the 9% Note nor any other document related thereto (the “Real Estate Documents”)
shall (1) be amended in a manner adverse to the interests of the Bank hereunder without
Bank’s prior written consent and (2) be secured by any Collateral other than the Property
(as defined in the Deed of Trust).

3. Limitation of Amendments.

3.1 The amendments set forth in Section 2, above, are effective for the purposes set
forth herein and shall be limited precisely as written and shall not be deemed to (a) be a
consent to any amendment, waiver or modification of any other term or condition of any Loan
Document, or (b) otherwise prejudice any right or remedy which Bank may now have or may have
in the future under or in connection with any Loan Document.

3.2 This Amendment shall be construed in connection with and as part of the Loan
Documents and all terms, conditions, representations, warranties, covenants and agreements
set forth in the Loan Documents, except as herein amended, are hereby ratified and confirmed
and shall remain in full force and effect.

4. Representations and Warranties. To induce Bank to enter into this Amendment,
Borrower hereby represents and warrants to Bank as follows:

4.1 Immediately after giving effect to this Amendment (a) the representations and
warranties contained in the Loan Documents are true, accurate and complete in all material
respects as of the date hereof (except to the extent such representations and warranties
relate to an earlier date, in which case they are true and correct as of such date), and (b)
no Event of Default has occurred and is continuing;

4.2 Borrower has the power and authority to execute and deliver this Amendment and to
perform its obligations under the Loan Agreement, as amended by this Amendment;

4.3 The organizational documents of Borrower delivered to Bank on the Effective Date
remain true, accurate and complete and have not been amended, supplemented or restated and
are and continue to be in full force and effect;

4.4 The execution and delivery by Borrower of this Amendment and the performance by
Borrower of its obligations under the Loan Agreement, as amended by this Amendment, have
been duly authorized;

4.5 The execution and delivery by Borrower of this Amendment and the performance by
Borrower of its obligations under the Loan Agreement, as amended by this Amendment, do not
and will not contravene (a) any law or regulation binding on or affecting Borrower, (b) any
contractual restriction with a Person binding on Borrower, (c) any order, judgment or decree
of any court or other governmental or public body or authority, or subdivision thereof,
binding on Borrower, or (d) the organizational documents of Borrower;

4.6 The execution and delivery by Borrower of this Amendment and the performance by
Borrower of its obligations under the Loan Agreement, as amended by this Amendment, do not
require any order, consent, approval, license, authorization or validation of, or filing,
recording or registration with, or exemption by any governmental or public body or
authority, or subdivision thereof, binding on either Borrower, except as already has been
obtained or made; and

4.7 This Amendment has been duly executed and delivered by Borrower and is the binding
obligation of Borrower, enforceable against Borrower in accordance with its terms, except as
such enforceability may be limited by bankruptcy, insolvency, reorganization, liquidation,
moratorium or other similar laws of general application and equitable principles relating to
or affecting creditors’ rights.

5. Counterparts. This Amendment may be executed in any number of counterparts and all
of such counterparts taken together shall be deemed to constitute one and the same
instrument.

6. Effectiveness. This Amendment shall be deemed effective upon (a) the due execution
and delivery to Bank of this Amendment by each party hereto, (b) of a fully executed
Subordination Agreement, (c) Borrower’s payment of a loan fee in an amount equal to $2,500
and (d) receipt of a fully executed mortgagee waiver and consent in the form of Exhibit B
hereto.

In Witness Whereof, the parties hereto have caused this Amendment to be duly executed
and delivered as of the date first written above.

	 	 	 
	BANK	 	BORROWER
	Silicon Valley Bank

By: /s/ Tom Smith

	 	Sipex Corporation

By: /s/ Clyde R. Wallin
	 

	 	 
	Name: Tom Smith

Title: Senior Relationship Manager

	 	Name: Clyde R. Wallin

Title: Sr. VP Finance & CFO
	 
	 	 

1

EXHIBIT A

SUBORDINATION AGREEMENT

Silicon Valley Bank

Subordination Agreement

	 	 	 
	Creditor:

	 	

	Rodfre Holdings LLC

Address: c/o Joe Prudente

Future Electronics Corp.

	 	

Borrower:
	41 Main Street

Bolton, MA 01740

	 	Sipex Corporation

Date: January 19, 2006
	
 
	 	 

This Subordination Agreement is entered into between SILICON VALLEY BANK (“Silicon”), whose
address is 3003 Tasman Drive, Santa Clara, California 95054, and the creditor named above (the
“Creditor”).

1. Subordination. To induce Silicon in its discretion to extend or continue to
extend credit to the above-named borrower (the “Borrower”) at any time, in such manner, upon such
terms and for such amounts as may be mutually agreeable to Silicon and the Borrower (but without
obligation on Silicon’s part to do so), the Creditor hereby agrees to subordinate and does hereby
subordinate payment by the Borrower of any and all indebtedness of the Borrower, now or hereafter
incurred, created or evidenced, to the Creditor, however such indebtedness may be hereafter
extended, renewed or evidenced (together with all guarantees, if any, for the payment of any such
indebtedness) (collectively, the “Junior Debt”), to the payment in full in cash to Silicon of any
and all present and future indebtedness, liabilities, guarantees and other obligations, of every
kind and description, of the Borrower to Silicon (collectively, the “Senior Debt”), and other than
a delivery of a notice of default or acceleration of such Junior Debt, the Creditor agrees not to
ask for, demand, sue for, take or receive any payments with respect to all or any part of the
Junior Debt, unless and until all of the Senior Debt have been paid and performed in full, except
that the following payments with respect to the Junior Debt may be made (the “Permitted Payments”)
and the following remedies may be exercised:

(a) If Borrower sells the property located at 233 South Hillview Drive, Milpitas, California 95035
(the “Property”) and, then Borrower may pay the net proceeds from the sale to Creditor in payment
of the principal, accrued and unpaid interest and other amounts due under the 9% Secured Note with
Convertible Interest Due January 19, 2008 (the “Subordinated Note”);

(b) so long as no Standstill Period (as defined below) or Blockage Period (as defined below) is in
effect, Creditor may exercise any remedy, including foreclosure, against the Property and apply the
net proceeds of the exercise of any such remedy to the payment of the principal, accrued and unpaid
interest and other amounts due under the Subordinated Note; and

(c) Notwithstanding any Blockage Period or Standstill Period, Creditor shall be entitled to
exercise any right it may now or in the future have to convert any or all of the Principal amount
of and/or accrued interest on the Junior Debt into stock of the Borrower (which stock shall not be
redeemable prior to the maturity date of the Senior Debt) and such conversion shall not constitute
a payment received in breach of this Agreement.

“Blockage Period” shall mean a period of time beginning on the delivery date of a written notice
from Silicon to which Creditor is notified of the occurrence of a default under the Senior Debt (a
“Senior Default Notice”) and terminating on the date, if any, of the earliest to occur of: (a)
Silicon’s written consent to such termination; or (b) the cure to the satisfaction of Silicon of
such default which is the basis for the applicable Blockage Period; or (c) 60 days after the
delivery date of a Senior Default Notice.

The word “indebtedness” is used herein in its most comprehensive sense and includes without
limitation any and all present and future loans, advances, credit, debts, obligations, liabilities,
representations, warranties, and guarantees, of any kind and nature, absolute or contingent,
liquidated or unliquidated, and individual or joint; but shall exclude any indebtedness of Borrower
to Creditor that do not arise under the Subordinated Note, the Deed of Trust and the documents
executed in connection therewith. Creditor represents and warrants to Silicon that the Borrower is
now indebted to the Creditor in the following amounts under the following described notes and/or
documents and that the same is all outstanding indebtedness owing from the Borrower to the
Creditor:

The principal amount of $7,000,000, together with accrued interest and other amounts due and owing
under the Subordinated Note and the Deed of Trust with Assignment of Rents dated as of January 19,
2006 among the Borrower, First American Title Insurance Company and Creditor.

Creditor represents and warrants that the Junior Debt is not, and will not be, secured by any
assets of the Borrower (other than the Property and the direct proceeds of the property), and if
for any reason Creditor takes or receives any collateral or security for any of the Junior Debt
(other than the Property), without limiting Silicon’s other rights and remedies, the security
interest of Creditor in such collateral and security shall in all respects be subordinate and
subject to all present and future security interests of Silicon therein, and Creditor shall not
collect, take possession of, foreclose upon, or exercise any other rights or remedies with respect
to, any collateral or security, judicially or non-judicially, or attempt to do any of the
foregoing. As of the date hereof, Silicon represents and warrants that the Senior Debt is not
secured by the Property other than the proceeds thereof.

2. Distribution of Assets. The Creditor and Silicon agree that upon any distribution of the
assets or readjustment of the indebtedness of the Borrower whether by reason of liquidation,
composition, bankruptcy, arrangement, receivership, assignment for the benefit of creditors or any
other action or proceeding involving the readjustment of all or any of the Junior Debt, or the
application of the assets of the Borrower to the payment or liquidation thereof, Silicon shall be
entitled to receive payment in full in cash of all of the Senior Debt prior to the payment of all
or any part of the Junior Debt, and in order to enable Silicon to enforce its rights hereunder in
any such action or proceeding, provided, however, that with any assets described in Sections 1(a)
or 1(b) shall be distributed first to Creditor in payment of the Junior Debt before any remaining
assets are delivered to Silicon for application to the Senior Debt.

3. Transfer of Subordinated Debt. The Creditor shall not sell, pledge, assign or otherwise
transfer, at any time while this Agreement remains in effect, any rights, claim or interest of any
kind in or to any of the Junior Debt, either principal or interest, without first notifying Silicon
and making such transfer expressly subject to this Subordination Agreement in form and substance
satisfactory to Silicon. The Creditor represents and warrants to Silicon that the Creditor has not
sold, pledged, assigned or otherwise transferred any of the Junior Debt, or any interest therein or
collateral or security therefor, or given any other subordination agreement in respect thereof, to
any other person. The Creditor will concurrently endorse all notes and other written evidence of
the Junior Debt with a statement that they are subordinated to the Senior Debt pursuant to the
terms of this Agreement, in such form as Silicon shall require, and the Creditor will exhibit the
originals of such notes and other written evidence of the Junior Debt to Silicon so that Silicon
can confirm that such endorsement has been made (but no failure to do any of the foregoing shall
affect the subordination of the Junior Debt provided for herein, which shall be fully effective
upon execution of this Agreement).

4. Default. The Creditor shall promptly give Silicon written notice of any default or
event of default (a “Notice of Junior Debt Default”) under any document, instrument or agreement
evidencing or relating to any of the Junior Debt, and, until the earlier of (a) the payment in full
of the Senior Debt or (b) 60 days after delivery of the Notice of Junior Debt Default (the
“Standstill Period”), the Creditor shall not commence or join in any action or proceeding to
recover any amounts due on the Junior Debt, commence or join in any involuntary bankruptcy
petition, insolvency proceeding or similar judicial proceeding against the Borrower, or collect,
accept payment on or security for, or exercise any other rights or remedies with respect to, the
Junior Debt, judicially or non-judicially, or attempt to do any of the foregoing, except for
Permitted Payments under Sections 1(a) and 1(c) above.

5. Silicon’s Rights. This is a continuing agreement of subordination and Silicon may
continue, without notice to the Creditor, to extend credit or other accommodation or benefit and
loan monies to or for the account of the Borrower in reliance hereon. Silicon may at any time, in
its discretion, renew or extend the time of payment of all or any Senior Debt, modify the Senior
Debt and any terms or provisions thereof or of any agreement relating thereto, waive or release any
collateral which may be held therefor at any time, and make and enter into any such agreement or
agreements as Silicon may deem proper or desirable relating to the Senior Debt, without notice to
or further consent from the Creditor and without any manner impairing or affecting this Agreement
or any of Silicon’s rights hereunder. The Creditor waives notice of acceptance hereof, notice of
the creation of any Senior Debt, the giving or extension of any credit by Silicon to the Borrower,
or the taking, waiving or releasing of any security therefor, or the making of any modifications,
and the Creditor waives presentment, demand, protest, notice of protest, notice of default, and all
other notices to which the Creditor might otherwise be entitled.

6. Revivor. If, after payment of the Senior Debt, the Borrower thereafter becomes liable to
Silicon on account of the Senior Debt, or any payment made on the Senior Debt shall for any reason
be returned by Silicon, this Agreement shall thereupon in all respects become effective with
respect to such subsequent or reinstated Senior Debt, without the necessity of any further act or
agreement between Silicon and the Creditor.

7. General. This Agreement sets forth in full all of the representations and agreements of
the parties with respect to the subject matter hereof and supersedes all prior discussions,
representations, agreements and understandings between the parties. This Agreement may not be
modified or amended, nor may any rights hereunder be waived, except in a writing signed by the
parties hereto. In the event of any litigation between the parties based upon, arising out of, or
in any way relating to this Agreement, the prevailing party shall be entitled to recover all of his
costs and expenses (including without limitation attorneys’ fees) from the non-prevailing party.
The parties agree to cooperate fully with each other and take all further actions and execute all
further documents from time to time as may be reasonably necessary to carry out the purposes of
this Agreement. At Silicon’s option, all actions and proceedings based upon, arising out of or
relating in any way directly or indirectly to, this Agreement shall be litigated exclusively in
courts located within Santa Clara County, California, and Creditor consents to the jurisdiction of
any such court and consents to the service of process in any such action or proceeding by personal
delivery, first-class mail, or any other method permitted by law, and waives any and all rights to
transfer or change the venue of any such action or proceeding to any court located outside Santa
Clara County, California. This Agreement is being entered into, and shall be governed by the laws
of the State of California. This Agreement shall be binding upon the Creditor and its successors
and assigns and shall inure to the benefit of Silicon and Silicon’s successors and assigns.
Nothing herein is to be construed as limiting, precluding or subjecting to any restriction or
waiting period (including, but not limited to the Blockage Period and/or Standstill Period) any
present or future right of the Creditor to convert any or all of the Junior Debt, including
interest accruing thereon, into stock (which stock shall not be redeemable prior to the maturity
date of the Senior Debt)

8. Mutual Waiver of Jury Trial. SILICON AND CREDITOR EACH HEREBY WAIVE THE RIGHT TO TRIAL BY
JURY IN ANY ACTION OR PROCEEDING BASED UPON, ARISING OUT OF, OR IN ANY WAY RELATING TO: (I) THIS
AGREEMENT; OR (II) ANY OTHER PRESENT OR FUTURE INSTRUMENT OR AGREEMENT BETWEEN SILICON AND
CREDITOR; OR (III) ANY CONDUCT, ACTS OR OMISSIONS OF SILICON OR CREDITOR OR ANY OF THEIR DIRECTORS,
OFFICERS, EMPLOYEES, AGENTS, ATTORNEYS OR ANY OTHER PERSONS AFFILIATED WITH SILICON OR CREDITOR;
IN EACH OF THE FOREGOING CASES, WHETHER SOUNDING IN CONTRACT OR TORT OR OTHERWISE.

9. Judicial Reference. WITHOUT INTENDING IN ANY WAY TO LIMIT THE PARTIES’ AGREEMENT TO WAIVE
THEIR RESPECTIVE RIGHT TO A TRIAL BY JURY, IF THE ABOVE WAIVER OF THE RIGHT TO A TRIAL BY JURY IS
NOT ENFORCEABLE, THE PARTIES HERETO AGREE THAT ANY AND ALL DISPUTES OR CONTROVERSIES OF ANY NATURE
BETWEEN THEM ARISING AT ANY TIME SHALL BE DECIDED BY A REFERENCE TO A PRIVATE JUDGE, MUTUALLY
SELECTED BY THE PARTIES (OR, IF THEY CANNOT AGREE, BY THE PRESIDING JUDGE OF THE SANTA CLARA
SUPERIOR COURT) APPOINTED IN ACCORDANCE WITH CALIFORNIA CODE OF CIVIL PROCEDURE SECTION 638 (OR
PURSUANT TO COMPARABLE PROVISIONS OF FEDERAL LAW IF THE DISPUTE FALLS WITHIN THE EXCLUSIVE
JURISDICTION OF THE FEDERAL COURTS), SITTING WITHOUT A JURY, IN THE SUPERIOR COURT OF CALIFORNIA,
COUNTY OF SANTA CLARA; AND THE PARTIES HEREBY SUBMIT TO THE JURISDICTION OF SUCH COURT. THE
REFERENCE PROCEEDINGS SHALL BE CONDUCTED PURSUANT TO AND IN ACCORDANCE WITH THE PROVISIONS OF
CALIFORNIA CODE OF CIVIL PROCEDURE §§ 638 THROUGH 645.1, INCLUSIVE. THE PRIVATE JUDGE SHALL HAVE
THE POWER, AMONG OTHERS, TO GRANT PROVISIONAL RELIEF, INCLUDING WITHOUT LIMITATION, ENTERING
TEMPORARY RESTRAINING ORDERS, ISSUING PRELIMINARY AND PERMANENT INJUNCTIONS AND APPOINTING
RECEIVERS. IF DURING THE COURSE OF ANY DISPUTE, A PARTY DESIRES TO SEEK PROVISIONAL RELIEF, BUT A
JUDGE HAS NOT BEEN APPOINTED AT THAT POINT PURSUANT TO THE JUDICIAL REFERENCE PROCEDURES, THEN SUCH
PARTY MAY APPLY TO THE SUPERIOR COURT OF CALIFORNIA, COUNTY OF SANTA CLARA FOR SUCH RELIEF..

Creditor:

RODFRE HOLDINGS LLC

By     /s/ Joe Prudente      

	 	 	 	Joe Prudente, duly authorized

Silicon:

SILICON VALLEY BANK

By /s/ Tom Smith

	 	 	 	Title Senior Relationship Manager

BORROWER’S AGREEMENT

The undersigned Borrower hereby acknowledges receipt of a copy of the foregoing Subordination
Agreement and agrees not to pay any Junior Debt, except as provided therein. In the event Borrower
breaches this Agreement or any of the provisions of the foregoing Subordination Agreement, Borrower
agrees that, in addition to all other rights and remedies Silicon has, all of the Senior Debt
shall, at Silicon’s option and without notice or demand, become immediately due and payable, unless
Silicon expressly agrees in writing to waive such breach. No waiver by Silicon of any breach shall
be effective unless in writing signed by one of Silicon’s authorized officers, and no such waiver
shall be deemed to extend to or waive any other or subsequent breach. Borrower further agrees that
any default or event of default by Borrower on the Junior Debt or under any present or future
instrument or agreement between Borrower and the Creditor shall constitute a default and event of
default under all present and future instruments and agreements between Borrower and Silicon.
Borrower further agrees that, at any time and from time to time, the foregoing Subordination
Agreement may be altered, modified or amended by Silicon and the Creditor without notice to
Borrower and without further consent by Borrower.

Borrower:

SIPEX CORPORATION

By Clyde R. Wallin      

President or Vice President

2

EXHIBIT B

MORTGAGEE WAIVER AND CONSENT

THIS MORTGAGEE’S WAIVER AND CONSENT (“Waiver and Consent”) is made and entered into as of this
19th day of January, 2006 by and among Rodfre Holdings LLC (“Mortgagee”) and Silicon
Valley Bank (“Bank”).

	 	A.	 	Sipex Corporation (“Borrower”) is the owner of the real
property located at 233 South Hillview Drive, Milpitas, California 95035 (the
“Premises”).

	 	B.	 	Borrower has granted a mortgage (the “Deed of Trust”) on the
Premises to Mortgagee.

	 	C.	 	Bank has previously entered into a Loan and Security Agreement
(as amended, restated, modified and/or supplemented from time to time, the
“Loan Agreement”) with Borrower, and to secure the obligations arising under
such Loan Agreement, Borrower has granted to Bank a security interest in and
lien upon the Collateral (as defined in the Loan Agreement).

NOW, THEREFORE, in consideration of any financial accommodations extended by Bank to Borrower
at any time, and other good and valuable consideration the receipt and sufficiency of which is
hereby acknowledged, the parties agree as follows:

	 	1.	 	Mortgagee will use reasonable efforts to provide Bank with
written notice of any default by Borrower under the Deed of Trust and the
documents related thereto (the “Real Estate Documents”). No action by Bank
pursuant to this Waiver and Consent shall be deemed to be an assumption by Bank
of any obligation under the Deed of Trust, and, except as provided in
paragraphs 6 and 7 below, Bank shall not have any obligation to Mortgagee.
Mortgagee’s failure to provide any such notice shall not in any way restrict or
preclude Mortgagee’s exercise of its rights or remedies under the Real Estate
Documents.

	 	2.	 	Mortgagee acknowledges the validity of Bank’s lien on the
Collateral and, until such time as the obligations of Borrower to Bank are
indefeasibly paid in full, Mortgagee subordinates any interest in the
Collateral and agrees not to distrain or levy upon any Collateral or to assert
any lien, right of distraint or other claim against the Collateral until Bank
is paid in full.

	 	3.	 	Bank or its representatives or invitees may enter upon the
Premises at any time without any interference by Mortgagee to inspect or remove
any or all of the Collateral, including, without limitation, by public auction
or private sale pursuant to the provisions of paragraph 7 below.

	 	4.	 	For, and in consideration of the Bank’s undertaking and
covenant to pay occupancy at the then prevailing market rate, as determined by
the Mortgagee, acting reasonably, Mortgagee will permit Bank and its
representatives and invitees to occupy and remain on the Premises;
provided, that such period of occupation (the “Disposition Period”)
shall not exceed 60 days. If any injunction or stay is issued that prohibits
Bank from removing the Collateral, the commencement of the Disposition Period
will be deferred until such injunction or stay is lifted or removed.

	 	5.	 	During any Disposition Period, Bank and its representatives and
invitees may inspect, repossess, remove and otherwise deal with the Collateral,
and Bank may advertise and conduct public auctions or private sales of the
Collateral at the Premises, in each case without interference by Mortgagee or
liability of Bank to Mortgagee (other than as set forth in Section 8 below).
If Bank conducts a public auction or private sale of the Collateral at the
Premises, Bank shall use reasonable efforts to notify Mortgagee, first and to
hold such auction or sale in a manner which would not unduly disrupt
Mortgagee’s use of the Premises.

	 	6.	 	Bank shall promptly repair, at Bank’s expense, or reimburse
Mortgagee for any physical damage to the Premises actually caused by the
conduct of any auction or sale of Collateral on the Premises and any removal of
Collateral by or through Bank (ordinary wear and tear excluded). Bank shall
not be liable for any diminution in value of the Premises caused by the absence
of Collateral removed, and Bank shall not have any duty or obligation to remove
or dispose of any Collateral or any other property left on the Premises by
Borrower.

	 	7.	 	All notices hereunder shall be in writing, sent by certified
mail, return receipt requested or by telecopy, to the respective parties and
the addresses set forth on the signature page or at such other address as the
receiving party shall designate in writing.

	 	8.	 	This Waiver and Consent may be executed in any number of
several counterparts, shall be governed and controlled by, and interpreted
under, the laws of the State of California, and shall inure to the benefit of
Bank and its successors and assigns and shall be binding upon Mortgagee and its
successors and assigns (including any transferees of the Premises).

3

IN WITNESS WHEREOF, this Mortgagee Waiver and Consent is entered into as of the date first set
forth above.

	 	 	 	 	 
	c/o Joe Prudente	 	“MORTGAGEE”
	Future Electronics Corp.
	 	RODFRE HOLDINGS LLC

	41 Main Street
	 	By: RODFRE HOLDINGS LLC

	Boston, Massachusetts 01740
	 	 	—	 
	Telephone: 978-779-3000
	 	Name: /s/ Joe Prudente

	 
	 	 	 	 
	Facsimile: 978-779-3071
	 	Title: Director

	 
	 	 	 	 
	 
	 	“BANK”
	3003 Tasman Drive
	 	SILICON VALLEY BANK

	Santa Clara, California 95054
	 	By: /s/ Tom Smith

	Attention: ___________________________
	 	 	—	 
	Telephone:
	 	Name: Tom Smith

	 
	 	 	 	 
	Facsimile:
	 	Title:  Senior Relationship Manager

	 
	 	 	 	 

4

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