Document:

<PAGE>   1
                                                                    Exhibit 10.9

                       SECOND LOAN MODIFICATION AGREEMENT

         This Second Loan Modification Agreement is entered into as of
______________, effective as of __________________, by and between
SYNCHRONICITY, INC., a Massachusetts corporation with its principal place of
business at 201 Forest Street, Marlborough, Massachusetts 01752 (the "Borrower")
and SILICON VALLEY BANK, a California-chartered bank ("Bank"), with its
principal place of business at 3003 Tasman Drive, Santa Clara, CA 95054 and with
a loan production office located at Wellesley Office Park, 40 William Street,
Suite 350, Wellesley, MA 02481, doing business under the name "Silicon Valley
East".

1.       DESCRIPTION OF EXISTING INDEBTEDNESS. Among other indebtedness which
may be owing by Borrower to Bank, Borrower is indebted to Bank pursuant to a
loan arrangement dated as of February 20, 1998, evidenced by, among other
documents, a certain Loan and Security Agreement dated as of February 20, 1998
between Borrower and Bank (the "Loan Agreement"). The Loan Agreement established
in favor of the Borrower: (i) a working capital line of credit in the maximum
principal amount of Nine Hundred Thousand Dollars ($900,000.00) (the "Committed
Revolving Line"), and (ii) an equipment line of credit in the maximum principal
amount of Three Hundred Fifty Thousand Dollars ($350,000.00) (the "1998
Committed Equipment Line"). Capitalized terms used but not otherwise defined
herein shall have the same meaning as in the Loan Agreement.

Hereinafter, all indebtedness owing by Borrower to Bank shall be referred to as
the "Indebtedness".

2.       DESCRIPTION OF COLLATERAL. Repayment of the Indebtedness is secured by
the Collateral as described in the Loan Agreement (together with any other
collateral security granted to Bank, the "Security Documents").

Hereinafter, the Security Documents, together with all other documents
evidencing or securing the Indebtedness shall be referred to as the "Existing
Loan Documents".

3.       DESCRIPTION OF CHANGE IN TERMS.

         A.       Modification(s) to Loan Agreement.

                  1.       The Loan Agreement shall be amended by deleting the
                           following definition appearing in Section 1.1
                           thereof:

                                    "Committed Revolving Line" means a credit
                                    extension of up to One Million Five Hundred
                                    Thousand Dollars ($1,500,000.00).
                                    Notwithstanding the foregoing, the
                                    availability of Advances under the Committed
                                    Revolving Line shall be subject to the
                                    receipt by the Bank of satisfactory results,
                                    in the sole and absolute discretion of the
                                    Bank, of the Initial Audit of Borrower's
                                    Accounts pursuant to Section 6.3 hereof. If
                                    the results of the Initial Audit are not
                                    satisfactory to the Bank for any reason, the
                                    Bank may, at its discretion, reduce the
                                    amount of the Committed Revolving Line, or
                                    not make any Advances hereunder, except
                                    pursuant to terms satisfactory to the Bank."

                           and inserting in lieu thereof the following:

                                    "Committed Revolving Line" means a credit
                                    extension of up to Two Million Five Hundred
                                    Thousand Dollars ($2,500,000.00).
                                    Notwithstanding the foregoing, the
                                    availability of Advances under the Committed
                                    Revolving

<PAGE>   2
                                    Line shall be subject to the receipt by the
                                    Bank of satisfactory results, in the sole
                                    and absolute discretion of the Bank, of the
                                    Initial Audit of Borrower's Accounts
                                    pursuant to Section 6.3 hereof. If the
                                    results of the Initial Audit are not
                                    satisfactory to the Bank for any reason, the
                                    Bank may, at its discretion, reduce the
                                    amount of the Committed Revolving Line, or
                                    not make any Advances hereunder, except
                                    pursuant to terms satisfactory to the Bank."

                  2.       The Loan Agreement shall be amended by deleting the
                           following definition appearing in Section 1.1
                           thereof:

                                    "Current Liabilities" means, as of any
                                    applicable date, all amounts that should, in
                                    accordance with GAAP, be included as current
                                    liabilities on the consolidated balance
                                    sheet of Borrower, as at such date, plus, to
                                    the extent not already included therein, all
                                    outstanding Credit Extensions made under
                                    this Agreement, including all Indebtedness
                                    that is payable upon demand or within one
                                    year from the date of determination thereof
                                    unless such Indebtedness is renewable or
                                    extendable at the option of Borrower to a
                                    date more than one year from the date of
                                    determination, but excluding Subordinated
                                    Debt.

                           and inserting in lieu thereof:

                                    "Current Liabilities" means, as of any
                                    applicable date, all amounts that should, in
                                    accordance with GAAP, be included as current
                                    liabilities on the consolidated balance
                                    sheet of Borrower, as at such date, plus, to
                                    the extent not already included therein, all
                                    outstanding Credit Extensions made under
                                    this Agreement, including all Indebtedness
                                    that is payable upon demand or within one
                                    year from the date of determination thereof
                                    unless such Indebtedness is renewable or
                                    extendable at the option of Borrower to a
                                    date more than one year from the date of
                                    determination, but excluding Subordinated
                                    Debt and deferred revenue.

                  3.       The Loan Agreement shall be amended by deleting the
                           following definition appearing in Section 1.1
                           thereof:

                                    ""Revolving Maturity Date" means February
                                    19, 2000."

                           and inserting in lieu thereof:

                                    ""Revolving Maturity Date" means February
                                    19, 2001."

                  4.       The Loan Agreement shall be amended by deleting the
                           following text appearing as paragraph (a) of Section
                           2.1.3. thereof:

                                    "2.1.3 1999 Equipment Advances.

                           (a) Subject to and upon the terms and conditions of
                           this Agreement, at any time through January 15, 2000
                           (the "1999 Equipment Availability End Date"), Bank
                           agrees to make Equipment Advances (each an "Equipment
                           Advance" and

                                       2-
<PAGE>   3
                           collectively, the "Equipment Advances") to Borrower
                           under this Section 2.1.3 in an aggregate outstanding
                           amount not to exceed the 1999 Committed Equipment
                           Line. To evidence the Equipment Advances, Borrower
                           shall deliver to Bank, at the time of each Equipment
                           Advance request, an invoice for the equipment
                           purchased. The Equipment Advances under this Section
                           2.1.3 shall be used only to purchase Equipment and
                           shall not exceed One Hundred Percent (100%) of the
                           invoice amount of such equipment approved from time
                           to time by Bank, excluding taxes, shipping, warranty
                           charges, freight discounts and installation expense.
                           Software may only constitute up to Two Hundred Fifty
                           Thousand Dollars ($250,000.00) of aggregate Equipment
                           Advances under this Section 2.1.3.

                           and inserting in lieu thereof the following:

                           (a) Subject to and upon the terms and conditions of
                           this Agreement, at any time through August 16, 2000
                           (the "1999 Equipment Availability End Date"), Bank
                           agrees to make Equipment Advances (each an "Equipment
                           Advance" and collectively, the "Equipment Advances")
                           to Borrower under this Section 2.1.3 in an aggregate
                           outstanding amount not to exceed the 1999 Committed
                           Equipment Line. To evidence the Equipment Advances,
                           Borrower shall deliver to Bank, at the time of each
                           Equipment Advance request, an invoice for the
                           equipment purchased. The Equipment Advances under
                           this Section 2.1.3 shall be used only to purchase
                           Equipment and shall not exceed One Hundred Percent
                           (100%) of the invoice amount of such equipment
                           approved from time to time by Bank, excluding taxes,
                           shipping, warranty charges, freight discounts and
                           installation expense. Software may only constitute up
                           to Two Hundred Fifty Thousand Dollars ($250,000.00)
                           of aggregate Equipment Advances under this Section
                           2.1.3.

                  5.       The Loan Agreement shall be amended by deleting the
                           following text appearing as the fourth paragraph of
                           Section 6.3 thereof:

                                    "Bank shall have a right from time to time
                                    hereafter to audit Borrower's Accounts at
                                    Borrower's expense, provided that such
                                    audits will be conducted: (a) no more often
                                    than every twelve (12) months, and (b) only
                                    when either (i) Obligations under the
                                    Committed Revolving Line are outstanding or
                                    (ii) Advances were made during the preceding
                                    twelve (12) month period. Notwithstanding
                                    the foregoing, the Bank shall have the right
                                    to audit Borrower's Accounts at Borrower's
                                    expense at any time after the occurrence of
                                    an Event of Default. The initial Advance
                                    under the Committed Revolving Line shall be
                                    subject to satisfactory results, in the sole
                                    discretion of Bank, of an initial audit (the
                                    "Initial Audit") of Borrower's Accounts."

                           and inserting in lieu thereof the following:

                                    "Bank shall have a right from time to time
                                    hereafter to audit Borrower's Accounts at
                                    Borrower's expense, provided that such
                                    audits will be conducted: (a) no more often
                                    than every twelve (12) months, and (b) only
                                    when either (i) Obligations under the
                                    Committed Revolving Line are outstanding or
                                    (ii) Advances were made during the preceding
                                    twelve (12) month period. Notwithstanding
                                    the foregoing, the Bank shall have the right

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<PAGE>   4
                                    to audit Borrower's Accounts at Borrower's
                                    expense at any time after the occurrence of
                                    an Event of Default. Any Advance under the
                                    Committed Revolving Line which is in excess
                                    of twenty-five percent (25%) of the
                                    available Borrowing Base or when added to
                                    the aggregate outstanding Advances would
                                    result in the aggregate outstanding Advances
                                    being in excess of twenty-five percent (25%)
                                    of the available Borrowing Base, shall be
                                    subject to satisfactory results, in the sole
                                    discretion of Bank, of an initial audit (the
                                    "Initial Audit") of Borrower's Accounts."

                  6.       The Loan Agreement shall be amended by deleting the
                           following text appearing as Section 6.10 thereof:

                                    "6.10 Tangible Net Worth. Borrower shall
                                    maintain: (i) as of the last day of each
                                    quarter, a Tangible Net Worth of not less
                                    than Three Million Dollars ($3,000,000.00),
                                    and (ii) on a monthly basis, as of the last
                                    day of all months which are not the last
                                    month of a quarter, a Tangible Net Worth of
                                    not less than Two Million Five Hundred
                                    Thousand Dollars ($2,500,000.00)."

                           and inserting in lieu thereof the following:

                                    "6.10 Tangible Net Worth. Borrower shall
                                    maintain: (i) as of the last day of each
                                    month through May 31, 2000, a Tangible Net
                                    Worth of not less than Two Million Dollars
                                    ($2,000,000.00), and (ii) on a monthly
                                    basis, as of the last day of all months
                                    thereafter beginning on June 30, 2000, a
                                    Tangible Net Worth of not less than the
                                    greater of (a) Five Million Dollars
                                    ($5,000,000.00) or (b) the amount raised in
                                    any initial public offering or the next
                                    equity round."

                  7.       The Borrower hereby ratifies, confirms and reaffirms,
                           all and singular, the terms and conditions of a
                           certain Negative Pledge Agreement dated as of
                           February 20, 1998 between Borrower and Bank, and
                           acknowledges, confirms and agrees that said Negative
                           Pledge Agreement shall remain in full force and
                           effect.

                  8.       Bank hereby waives Borrower's existing Default under
                           the Loan Agreement by virtue of Borrower's failure to
                           comply with the Adjusted Quick Ratio and Tangible Net
                           Worth covenants at December 31, 1999. Bank's waiver
                           of Borrower's compliance of said covenants shall
                           apply only to the foregoing periods.

                           Bank's agreement to waive the above-described
                           compliance (i) shall not be deemed an agreement by
                           Bank to waive Borrower's compliance with either of
                           the above-described covenants as of any other dates,
                           (ii) shall not limit or impair Bank's right to demand
                           strict performance of either covenant as of any other
                           dates, and (iii) shall not limit or impair Bank's
                           right to demand strict performance of all other
                           covenants as of any date.

                  9.       The Compliance Certificate appearing as EXHIBIT D to
                           the Loan Agreement is hereby replaced with the
                           Compliance Certificate attached as EXHIBIT A hereto.

                                       4-
<PAGE>   5
4.       FEES. Borrower shall pay to Bank a fee equal to Five Thousand Dollars
         ($5,000.00), in connection with the modification of the Committed
         Revolving Line, which fee shall be due on the date hereof and shall be
         deemed fully earned as of the date hereof, and a fee equal to Two
         Thousand Five Hundred Dollars ($2,500.00), in connection with the
         modification of the 1999 Committed Equipment Line (the "Equipment Line
         Modification Fee"), which fee shall be due on the 1999 Equipment
         Availability End Date and shall be deemed fully earned as of the date
         hereof. Notwithstanding the foregoing, the Equipment Line Modification
         Fee shall be waived by Bank if on, or any time prior to the Equipment
         Availability End Date, the aggregate outstanding Equipment Advances
         equal at least Two Hundred Fifty Thousand Dollars ($250,000.00) The
         Borrower shall also reimburse Bank for all legal fees and expenses
         incurred in connection with this amendment to the Existing Loan
         Documents.

5.       RATIFICATION OF LOAN DOCUMENTS. Borrower hereby ratifies, confirms, and
reaffirms all terms and conditions of all security or other collateral granted
to the Bank, and confirms that the indebtedness secured thereby includes,
without limitation, the Indebtedness.

6.       NO DEFENSES OF BORROWER. Borrower agrees that, as of this date, it has
no defenses against the obligations to pay any amounts under the Indebtedness.

7.       CONTINUING VALIDITY. Borrower understands and agrees that in modifying
the existing Indebtedness, Bank is relying upon Borrower's representations,
warranties, and agreements, as set forth in the Existing Loan Documents. Except
as expressly modified pursuant to this Loan Modification Agreement, the terms of
the Existing Loan Documents remain unchanged and in full force and effect.
Bank's agreement to modifications to the existing Indebtedness pursuant to this
Loan Modification Agreement in no way shall obligate Bank to make any future
modifications to the Indebtedness. Nothing in this Loan Modification Agreement
shall constitute a satisfaction of the Indebtedness. It is the intention of Bank
and Borrower to retain as liable parties all makers of Existing Loan Documents,
unless the party is expressly released by Bank in writing. No maker will be
released by virtue of this Loan Modification Agreement.

8.       JURISDICTION/VENUE. Borrower accepts for itself and in connection with
its properties, unconditionally, the non-exclusive jurisdiction of any state or
federal court of competent jurisdiction in the Commonwealth of Massachusetts in
any action, suit, or proceeding of any kind against it which arises out of or by
reason of this Loan Modification Agreement; provided, however, that if for any
reason Bank cannot avail itself of the courts of the Commonwealth of
Massachusetts, then venue shall lie in Santa Clara County, California.

9.       COUNTERSIGNATURE. This Loan Modification Agreement shall become
effective only when it shall have been executed by Borrower and Bank (provided,
however, in no event shall this Loan Modification Agreement become effective
until signed by an officer of Bank in California).

                                       5-
<PAGE>   6
         This Second Loan Modification Agreement is executed as a sealed
instrument under the laws of the Commonwealth of Massachusetts as of the date
first written above.

BORROWER:                              BANK:

SYNCHRONICITY, INC.                    SILICON VALLEY BANK, doing business as
                                       SILICON VALLEY EAST

By:______________________________      By:___________________________________

Name: Joseph Calo                      Name: David E. Rodriguez

Title: Chief Financial Officer         Title: Vice President

                                       SILICON VALLEY BANK

                                       By:___________________________________

                                       Name:_________________________________

                                       Title:________________________________
                                          (signed in Santa Clara County,
                                           California)

                                       6-
<PAGE>   7
                                    EXHIBIT A

                             COMPLIANCE CERTIFICATE

TO:           SILICON VALLEY BANK

FROM:         SYNCHRONICITY, INC.

         The undersigned authorized officer of SYNCHRONICITY, INC. hereby
certifies that in accordance with the terms and conditions of the Loan and
Security Agreement between Borrower and Bank (the "Agreement"), (i) Borrower is
in complete compliance for the period ending      with all required covenants
except as noted below and (ii) all representations and warranties of Borrower
stated in the Agreement are true and correct in all material respects as of the
date hereof. Attached herewith are the required documents supporting the above
certification. The Officer further certifies that these are prepared in
accordance with Generally Accepted Accounting Principles (GAAP) and are
consistently applied from one period to the next except as explained in an
accompanying letter or footnotes. The Officer expressly acknowledges that no
borrowings may be requested by the Borrower at any time or date of determination
that Borrower is not in compliance with any of the terms of the Agreement, and
that such compliance is determined not just at the date this certificate is
delivered.

         PLEASE INDICATE COMPLIANCE STATUS BY CIRCLING YES/NO UNDER "COMPLIES"
COLUMN.

<TABLE>
<CAPTION>
         REPORTING COVENANT                          REQUIRED                                    COMPLIES
         ------------------                          --------                                    --------

<S>                                                  <C>                                         <C>
         Monthly financial statements & CC           Monthly within 25 days                      Yes      No
         Annual (CPA Audited)                        FYE within 120 days                         Yes      No
         Monthly BBC & A/R Agings                    Monthly within 25 days                      Yes      No
                                                     (when borrowing)
</TABLE>

<TABLE>
<CAPTION>
         FINANCIAL COVENANT                          REQUIRED                       ACTUAL       COMPLIES
         ------------------                          --------                       ------       --------

<S>                                                  <C>                            <C>          <C>
         Maintain:

         Quick Ratio (monthly)                       1.50:1.0                       _____:1.0    Yes      No
         Tangible Net Worth (monthly)                $2,000,000 as of 5/31/00      $_________    Yes      No
                                                     $5,000,000 or 25% of
                                                     the IPO/equity round,
                                                     whichever is greater
                                                     beginning 6/30/00 and
                                                     thereafter

         Minimum Liquidity (monthly)                 1.50:1.0                       _____:1.0    Yes      No
         OR Minimum Debt Service Coverage            1.25:1.0                       _____:1.0    Yes      No
</TABLE>

COMMENTS REGARDING EXCEPTIONS:

Sincerely,

_______________________          Date:_______________
SIGNATURE

_______________________

       BANK USE ONLY
RECEIVED
BY:_________________________
DATE:_______________________
REVIEWED
BY:_________________________
COMPLIANCE STATUS:  YES / NO

                                       7-<PAGE>   1
                                                                   Exhibit 10.10

                            NEGATIVE PLEDGE AGREEMENT

      This Negative Pledge Agreement is made as of February 20, 1998, by and
between SYNCHRONICITY, INC., a Massachusetts corporation with a chief executive
office located at 201 Forest Street, Marlborough, Massachusetts 01752
("Borrower") and SILICON VALLEY BANK, a California-chartered bank, with its
principal place of business at 3003 Tasman Drive, Santa Clara, California 95054
and with a loan production office located at Wellesley Office Park, 40 William
Street, Suite 350, Wellesley, Massachusetts 02181, doing business under the name
"Silicon Valley East" ("Bank")

In connection with, among other documents, the Loan and Security Agreement (the
"Loan Documents") being concurrently executed herewith between Borrower and
Bank, Borrower agrees as follows:

1.    Except for the granting of licenses by borrower in the ordinary course of
      business, Borrower shall not sell, transfer, assign, mortgage, pledge,
      lease, grant a security interest in, or encumber any of Borrower's
      Intellectual Property (as defined below):

2.    It shall be an event of default under the Loan Documents between Borrower
      and Bank if there is a breach of any term of this Negative Pledge
      Agreement.

3.    As used herein,

      (a) "Intellectual Property" means:

            (i)   Any and all Copyright rights, Copyright applications,
                  copyright registrations and like protections in each work or
                  authorship and derivative work thereof, whether published or
                  unpublished and whether or not the same also constitutes a
                  trade secret, now or hereafter existing, created, acquired or
                  held;

            (ii)  Any and all trade secrets, and any and all intellectual
                  property rights in computer software and computer software
                  products now or hereafter existing, created, acquired or held;

            (iii) Any and all design rights which may be available to Borrower
                  now or hereafter existing, created, acquired or held;

            (iv)  All Mask Works or similar rights available for the protection
                  of semiconductor chips;

            (v)   All Patents, Patent applications and like protections
                  including, without limitation, improvements, divisions,
                  continuations, renewals, reissues, extensions and
                  continuations-in-part of the same, including without
                  limitation the Patents and Patent applications;
<PAGE>   2

            (vi)  Any Trademark and servicemark rights, whether registered or
                  not, applications to register and registrations of the same
                  and like protections, and the entire goodwill of the business
                  of Borrower connected with and symbolized by such Trademarks;

            (vii) Any and all claims for damages by way of past, present and
                  future infringements of any of the rights included above, with
                  the right, but not the obligation, to sue for and collect such
                  damages for said use or infringement of the intellectual
                  property rights identified above;

            (viii) All licenses or other rights to use any of the Copyrights,
                  Patents, Trademarks, or Mask Works and all license fees and
                  royalties arising from such use to the extent permitted by
                  such license or rights; and

            (ix)  All amendments, extensions, renewals and extensions of any of
                  the Copyrights, Trademarks, Patents, or Mask Works; and

            (x)   All proceeds and products of the foregoing, including without
                  limitation all payments under insurance or any indemnity or
                  warranty payable in respect of any of the foregoing.

      (b)   "Copyrights" means any and all copyright rights, copyright
            applications, copyright registrations and like protections in each
            work or authorship and derivative work thereof, whether published or
            unpublished and whether or not the same also constitutes a trade
            secret, now or hereafter existing, created, acquired or held;

      (c)   "Mask Works" means all mask work or similar rights available for the
            protection of semiconductor chips, now owned or hereafter acquired;

      (d)   "Patents" means all patents, patent applications and like
            protections including without limitation improvements, divisions,
            continuations, renewals, reissues, extension and
            continuations-in-part of the same;

      (e)   "Trademarks" means any trademark and servicemark rights, whether
            registered or not, applications to register and registrations of the
            same and like protections, and the entire goodwill of the business
            of Borrower connected with and symbolized by such trademarks.

4.    Capitalized terms used but not otherwise defined herein shall have the
      same meaning as in the Loan Documents.

5.    The laws of the Commonwealth of Massachusetts shall apply to this
      Agreement. BORROWER ACCEPTS FOR ITSELF AND IN CONNECTION WITH ITS
      PROPERTIES, UNCONDITIONALLY, THE NON-EXCLUSIVE JURISDICTION OF ANY STATE
      OR FEDERAL COURT OF COMPETENT
<PAGE>   3

      JURISDICTION IN THE COMMONWEALTH OF MASSACHUSETTS IN ANY ACTION, SUIT, OR
      PROCEEDING OF ANY KIND, AGAINST IT WHICH ARISES OUT OF OR BY REASON OF
      THIS AGREEMENT; PROVIDED, HOWEVER, THAT IF FOR ANY REASON BANK CANNOT
      AVAIL ITSELF OF THE COURTS OF THE COMMONWEALTH OF MASSACHUSETTS, BORROWER
      ACCEPTS JURISDICTION OF THE COURTS AND VENUE IN SANTA CLARA COUNTY,
      CALIFORNIA.

6.    This Agreement shall become effective only when it shall have been
      executed by Borrower and Bank (provided, however, in no event shall this
      Agreement become effective until signed by an officer of Bank in
      California).

                                    BORROWER:

                                    SYNCHRONICITY, INC.

                                    By:     /s/ Eugene Connolly
                                       --------------------------------------
                                    Name:
                                         ------------------------------------
                                    Title:
                                          -----------------------------------

                                    BANK:

                                    SILICON VALLEY BANK d/b/a SILICON VALLEY
                                      EAST

                                    By:     /s/ Carolyn Macedo
                                       --------------------------------------
                                    Name:
                                         ------------------------------------
                                    Title:
                                          -----------------------------------

                                    SILICON VALLEY BANK

                                    By:     /s/ Michelle Giannini
                                       --------------------------------------
                                    Name:
                                         ------------------------------------
                                    Title:
                                          -----------------------------------
                                          (Signed in Santa Clara, California)

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