Property, plant and equipment, net includes $3.4 million and $3.1 million of machinery and equipment under capital leases as of June 30, 2017 and December 31, 2016, respectively. Accumulated amortization of assets under capital leases totaled $0.3 million and $0.6 million as of June 30, 2017 and December 31, 2016, respectively.

Depreciation and amortization expense, including amortization of assets under capital leases was $2.7 million and $2.8 million for the three months ended June 30, 2017 and 2016, respectively, and $5.4 million and $5.7 million for the six months ended June 30, 2017 and 2016, respectively.

2014 Rule 144A Convertible Note Offering

In May 2014, the Company sold $75.0 million aggregate in principal amount of 6.50% Convertible Senior Notes due 2019 (or the 2014 144A Notes) to certain qualified institutional buyers in a private placement. The net proceeds from the offering were $72.0 million after payment of the initial purchaser’s discounts and offering expenses. Certain of the Company's affiliated entities purchased $24.7 million in aggregate principal amount of 2014 144A Notes (described further below under "Related Party Convertible Notes"), including $9.7 million by Total in the form of cancellation of existing indebtedness. In October 2015, the Company issued $57.6 million of convertible senior notes (as described below under “2015 Rule 144A Convertible Note Offering”) and used $18.3 million of the net proceeds therefrom to repurchase $22.9 million aggregate principal amount of outstanding 2014 144A Notes. The 2014 144A Notes bear interest at a rate of 6.50% per year, payable semiannually in arrears on May 15 and November 15 of each year. The 2014 144A Notes mature on May 15, 2019, unless earlier converted or repurchased. The 2014 144A Notes are convertible into shares of the Company's common stock at a conversion rate of 17.8073 shares of common stock per $1,000 principal amount of 2014 144A Notes (subject to adjustment in certain circumstances), representing an effective initial conversion price of approximately $56.16 per share of common stock. Refer to the “Exchange” and “Maturity Treatment Agreement” sections of this Note 5, "Debt and Mezzanine Equity" for details of the impact of the Maturity Treatment and Exchange Agreements on the 2014 144A Notes.

2015 Rule 144A Convertible Note Offering

In October 2015, the Company sold $57.6 million aggregate principal amount of 9.50% Convertible Senior Notes due 2019 (or the 2015 144A Notes) to certain qualified institutional buyers in a private placement. The net proceeds from the offering of the 2015 144A Notes were $54.4 million after payment of the offering expenses and placement agent fees. The Company used $18.3 million of the net proceeds to repurchase $22.9 million aggregate principal amount of outstanding 2014 144A Notes and $8.8 million to repurchase $9.7 million aggregate principal amount of outstanding Fidelity Notes, in each case held by purchasers of the 2015 144A Notes. The 2015 144A Notes bear interest at a rate of 9.50% per year, payable semiannually in arrears on April 15 and October 15 of each year. Interest on the 2015 144A Notes is payable, at the Company’s option, entirely in cash or entirely in common stock. The Company elected to make the April 15, 2016 interest payment in shares of common stock, the October 15, 2016 interest payment in cash and the April 15, 2017 interest payment in shares of common stock. The 2015 144A Notes will mature on April 15, 2019 unless earlier converted or repurchased.

The 2015 144A Notes are convertible into shares of the Company's common stock at a conversion rate of 48.3395 shares of Common Stock per $1,000 principal amount of 2015 144A Notes as of June 6, 2017, representing an effective conversion price of approximately $20.69 per share of common stock. Upon conversion, noteholders are entitled to receive a payment equal to the present value of the remaining scheduled payments of interest on the 2015 144A Notes being converted through maturity (April 15, 2019), computed using a discount rate of 0.75%. The Company may make such payment (the “Early Conversion Payment”) either in cash or in common stock, at its election subject to certain conditions, with the stock valued at 92.5% of the simple average of the daily volume-weighted average price per share for the 10 trading days ending on and including the trading day immediately preceding the conversion date. Through June 30, 2017, the Company has elected to make each Early Conversion Payment in shares of common stock. In January 2017, the Company issued an additional $19.1 million in aggregate principal amount of 2015 144A Notes (or the Additional 2015 144A Notes) in exchange for the cancellation of $15.3 million in aggregate principal amount of outstanding Fidelity Notes. Unless and until the Company obtains stockholder approval to issue a number of shares of the Company’s common Stock in excess of the Additional 2015 144A Notes Exchange Cap (as defined below), holders of the Additional 2015 144A Notes will not have the right to receive shares of the Company’s common stock upon conversion of the Additional 2015 144A Notes, and the Company will not have the right to issue shares of common stock as payment of interest on the Additional 2015 144A Notes, including any Early Conversion Payment, if the aggregate number of shares issued with respect to the Additional 2015 144A Notes (and any other transaction aggregated for such purpose) after giving effect to such conversion or payment, as applicable, would exceed 19.99% of the number of shares of the Company’s common stock outstanding as of December 28, 2016 (or the Additional 2015 144A Notes Exchange Cap). The Company will pay cash in lieu of any shares that would otherwise be deliverable in excess of the Additional 2015 144A Notes Exchange Cap.

May 2016 Convertible Note Offering

In May 2016, the Company entered into a securities purchase agreement (or the May 2016 Purchase Agreement) between the Company and a private investor relating to the sale of up to $15.0 million aggregate principal amount of convertible notes (or the May 2016 Convertible Notes).

Pursuant to the May 2016 Purchase Agreement, the full amount of the May 2016 Convertible Notes was issued in three separate closing in May 2016, September, 2016 and October 2016 for net proceeds of $14.9 million.

The May 2016 Convertible Notes were fully repaid in October 2016.

December 2016 and April 2017 Convertible Note Offerings

On December 1, 2016, the Company entered into a securities purchase agreement (or the December 2016 Purchase Agreement) with a private investor (or the Purchaser) and issued and sold a convertible note in principal amount $10.0 million (or the December 2016 Convertible Note) to the Purchaser, resulting in net proceeds to the Company of $9.9 million. The December 2016 Convertible Note was fully repaid in May 2017.

On April 13, 2017, the Company entered into a securities purchase agreement (or the April 2017 Purchase Agreement) with the Purchaser relating to the sale of up to an additional $15.0 million aggregate principal amount of convertible notes (or the April 2017 Convertible Notes). The April 2017 Purchase Agreement provides the Purchaser with a right of first refusal with respect to any variable rate transaction, subject to certain exceptions, on the same terms and conditions as are offered to a third-party purchaser for as long as the Purchaser holds any April 2017 Convertible Notes or shares of common stock underlying the April 2017 Convertible Notes.

On April 17, 2017, the Company issued and sold an April 2017 Convertible Note in the principal amount of $7.0 million (or the $7 Million Note) to the Purchaser, for proceeds to the Company of $6.9 million. The $7 Million Note was fully repaid in May 2017.

On May 2, 2017, in connection with the Purchaser agreeing to extend the time period for certain obligations of the Company under the April 2017 Purchase Agreement, the Company and the Purchaser entered into an Amendment Agreement (or the Amendment Agreement) with respect to the December 2016 Purchase Agreement, the April 2017 Purchase Agreement, the December 2016 Convertible Note and the April 2017 Convertible Notes (or the Amended Notes), pursuant to which the Company and the Purchaser agreed, among other things, to amend the December 2016 Convertible Note and the April 2017 Convertible Notes to (i) reduce the price at which the Company may pay monthly installments under the Amended Notes in shares of common stock from a 10% discount to a market-based price to a 20% discount to a market-based price and (ii) reduce the price floor related to any such payment from 80% of, in the case of the December 2016 Convertible Note, the volume-weighted average price per share (or VWAP) of the Company’s common stock on the trading day immediately preceding the applicable installment date and, in the case of the April 2017 Convertible Notes, the arithmetic average of the VWAP of the Company’s common stock for the five trading days immediately preceding the applicable installment date, to 70% of the arithmetic average of the VWAP of the Company’s common stock for the five trading days immediately preceding the applicable installment date.

On June 30, 2017, the Company issued and sold an Amended Note under the April 2017 Purchase Agreement in the principal amount of $3.0 million (or the $3 Million Note) to the Purchaser, for proceeds to the Company of $3.0 million. In connection with the issuance and sale of the $3 Million Note, the Company and the Purchaser entered into a letter agreement, pursuant to which, among other things, the Purchaser has the right to cause the Company to redeem all of the outstanding principal amount of the $3 Million Note in cash in accordance with the redemption provisions set forth in the $3 Million Note, as described below, upon the written request of the Purchaser within 10 days after the Company publicly announces the closing of the Second Tranche Funding (as defined below). See Note 14, “Subsequent Events”, for more details.

The Amended Notes are general unsecured obligations of the Company. Unless earlier converted or redeemed, the Amended Notes will mature on or about the 18-month anniversary of their respective issuance, subject to the rights of the holders to extend the maturity date in certain circumstances.

The Amended Notes are payable in monthly installments, in either cash at 118% of such installment amount or, at the Company’s option, subject to the satisfaction of certain equity conditions, shares of common stock at a discount to the then-current market price, subject to a price floor, as described above. In addition, in the event that the Company elects to pay all or any portion of a monthly installment in common stock, the holders of the Amended Notes have the right to require that the Company repay in common stock an additional amount of the Amended Notes not to exceed 50% of the cumulative sum of the aggregate amounts by which the dollar-weighted trading volume of the common stock for all trading days during the applicable installment period exceeds $200,000.

The Amended Notes contain customary terms and covenants, including certain events of default after which the holders may require the Company to redeem all or any portion of their Amended Notes in cash at a price equal to the greater of (i) 118% of the amount being redeemed and (ii) the intrinsic value of the shares of common stock issuable upon an installment payment of the amount being redeemed in shares.

In the event of a Fundamental Transaction (as defined in the Amended Notes), holders of the Amended Notes may require the Company to redeem all or any portion of their Amended Notes at a price equal to the greater of (i) 118% of the amount being redeemed and (ii) the intrinsic value of the shares of common stock issuable upon an installment payment of the amount being redeemed in shares.

The Company has the right to redeem the Amended Notes for cash, in whole, at any time, or in part, from time to time, at a redemption price equal to 118% of the principal amount of the Amended Notes to be redeemed.

The Amended Notes are convertible from time to time, at the election of the holders, into shares of common stock at an conversion price of $28.50 per share.

Notwithstanding the foregoing, the holders will not have the right to convert any portion of an Amended Note, and the Company will not have the option to pay any amount in shares of common stock, if (a) the holder, together with its affiliates, would beneficially own in excess of 4.99% (or such other percentage as determined by the holder and notified to the Company in writing, not to exceed 9.99%, provided that any increase of such percentage will not be effective until 61 days after notice thereof) of the number of shares of common stock outstanding immediately after giving effect to such conversion or payment, as applicable, or (b) the aggregate number of shares issued with respect to the Amended Notes (and any other transaction aggregated for such purpose) after giving effect to such conversion or payment, as applicable, would exceed 3,792,779 shares of common stock (or the Amended Notes Exchange Cap). In the event that the Company is prohibited from issuing any shares of common stock under the Amended Notes as a result of the Amended Notes Exchange Cap, the Company will pay cash in lieu of any shares that would otherwise be deliverable in excess of the Amended Notes Exchange Cap. In addition, pursuant to the April 2017 Purchase Agreement, in the event that the aggregate number of shares of common stock issuable with respect to the April 2017 Convertible Notes (and any other transaction aggregated for such purpose) would equal or exceed 218,817 of shares of common stock, the Company will be required to take all actions necessary for, and use its reasonable best efforts to solicit and obtain, stockholder approval for the issuance of shares of common stock in excess of the Amended Notes Exchange Cap.

For as long as they hold Amended Notes or shares of common stock issued under the Amended Notes, the holders may not sell any shares of common stock at a price less than $15.75 per share; provided, that with respect to any shares of common stock issued under the Amended Notes at a price less than $15.00, the holders may sell such shares at a price not less than the price floor applicable to the installment period with respect to which such shares were issued.

As of June 30, 2017, the balance of the Amended Notes was $19.1 million. At December 31, 2016, the balance of the December 2016 Convertible Note was $9.9 million.

See Note 14, “Subsequent Events”, for details regarding financing transactions completed subsequent to June 30, 2017.

Related Party Convertible Notes

Total R&D Convertible Notes

In July 2012 and December 2013, the Company entered into a series of agreements (or the Total Fuel Agreements) with an affiliate of Total S.A. (or, together with its affiliates, Total) to, among other things, establish (i) a research and development program and (ii) a convertible debt structure for the collaboration funding for the program from Total. The purchase agreement for the notes related to the collaboration funding from Total provided for the purchase and sale of an aggregate of $105.0 million of 1.5% Senior Convertible Notes due March 2017 (or the R&D Notes), which by January 2015 had been fully funded by Total.

In July 2015, Total exchanged all but $5.0 million of the R&D Notes then held by Total, such canceled notes having an aggregate principal amount of $70 million, in exchange for approximately 2.0 million shares of the Company’s common stock in connection with the Exchange. Refer to the “Exchange” section of this Note 5, "Debt and Mezzanine Equity", for additional details of the impact of the Exchange on the R&D Notes.

In March 2016, in connection with the restructuring of Total Amyris BioSolutions B.V. (or TAB), the fuels joint venture between the Company and Total, the Company sold to Total one half of the Company’s ownership stake in TAB (giving Total an aggregate ownership stake of 75% of TAB and giving the Company an aggregate ownership stake of 25% of TAB) in exchange for Total canceling (i) $1.3 million of the remaining R&D Notes, plus all paid-in-kind and accrued interest under all outstanding R&D Notes ($2.8 million, including all such interest that was outstanding as of July 29, 2015) and (ii) a note in the principal amount of Euro 50,000, plus accrued interest, issued to Total in connection with the original capitalization of TAB, and in connection therewith, Total surrendered to the Company the remaining R&D Note of $5.0 million in principal amount, and the Company executed and delivered to Total a new R&D Note in the principal amount of $3.7 million (or the Remaining R&D Note), with substantially similar terms and conditions to the previous R&D Notes other than it is unsecured and its payment terms are severed from TAB’s business performance. The disposal of the 25% ownership stake in TAB resulted in a gain to the Company of $4.2 million, which was recognized as a capital contribution from Total within equity.

As of June 30, 2017 and December 31, 2016, $3.7 million and $3.7 million, respectively, of the Remaining R&D Note were outstanding.

In February 2017, the Company and Total amended the Remaining R&D Note to extend the maturity of the Remaining R&D Note from March 1, 2017 to May 15, 2017. Subsequently, in May 2017, the Company and Total entered into a second amendment of the Remaining R&D Note, pursuant to which the parties agreed (i) to extend the maturity date of the Remaining R&D Note from May 15, 2017 to March 31, 2018, (ii) to increase the interest rate on the amounts outstanding under the Remaining R&D Note from 1.5% to 12.0%, beginning May 16, 2017, together with a corresponding increase to the default interest rate, and (iii) that accrued and unpaid interest on the amounts outstanding under the Remaining R&D Note will be payable on December 31, 2017 and the maturity date. The Remaining R&D Note is convertible into the Company’s common stock, at a conversion price of $46.20 per share, (i) within 10 trading days prior to maturity, (ii) on a change of control of the Company, and (iii) on a default by the Company. The conversion price of the Remaining R&D Note is subject to adjustment for proportional adjustments to outstanding common stock and under anti-dilution provisions in case of certain dividends and distributions.

August 2013 Financing Convertible Notes

In August 2013, the Company entered into a Securities Purchase Agreement (or the August 2013 SPA) with Total and Maxwell (Mauritius) Pte Ltd (or Temasek) to sell up to $73.0 million in convertible promissory notes in private placements (or the August 2013 Financing), with such notes to be sold and issued over a period of up to 24 months from the date of signing.

In October 2013, the Company sold and issued a senior secured promissory note to Temasek (or the Temasek Bridge Note) in exchange for a bridge loan of $35.0 million due on February 2, 2014 at an interest rate of 5.5% quarterly. The Temasek Bridge Note was canceled on October 16, 2013 as payment for Temasek’s purchase of Tranche I Notes in the first tranche of the August 2013 Financing, as further described below.

In October 2013, the Company amended the August 2013 SPA to include the investment by certain entities affiliated with FMR LLC in the first tranche of the August 2013 Financing of $7.6 million, and to proportionally increase the amount of first tranche notes acquired by exchange and cancellation of outstanding R&D Notes held by Total in connection with its exercise of pro rata rights up to $9.2 million in the first tranche. Also in October 2013, the Company completed the closing of the first tranche of senior convertible notes provided for in the August 2013 Financing (or the Tranche I Notes), issuing a total of $51.8 million in Tranche I Notes for cash proceeds of $7.6 million and exchange and cancellation of outstanding convertible promissory notes of $44.2 million, of which $35.0 million resulted from the exchange and cancellation of the Temasek Bridge Note and the remaining $9.2 million from the exchange and cancellation of an outstanding R&D Note held by Total. As a result of the exchange and cancellation of the $35.0 million Temasek Bridge Note and the $9.2 million R&D Note held by Total for the Tranche I Notes, the Company recorded a loss from extinguishment of debt of $19.9 million. The Tranche I Notes are due sixty months from the date of issuance (October 16, 2018) and were initially convertible into the Company’s common stock at a conversion price equal to $2.44 per share, which represented a 15% discount to the trailing 60-day weighted-average closing price of the common stock on The NASDAQ Stock Market (or NASDAQ) through August 7, 2013, subject to certain adjustments as described below. Interest accrues on the Tranche I Notes at a rate of 5% per six months, compounded semiannually, and is payable in kind by adding to the principal every six months or in cash. Through June 30, 2017, the Company has elected to pay interest on the Tranche I Notes in kind. The Tranche I Notes may be prepaid by the Company without penalty or premium every six months at the date of payment of the semi-annual coupon.

In December 2013, the Company further amended the August 2013 SPA to sell $3.0 million of senior convertible notes under the second tranche of the August 2013 Financing (or the Tranche II Notes) to funds affiliated with Wolverine Asset Management, LLC (or Wolverine). In January 2014, the Company sold and issued $34.0 million of Tranche II Notes in the second tranche of the August 2013 Financing, with Temasek purchasing $25.0 million of the Tranche II Notes and funds affiliated with Wolverine purchasing $3.0 million of the Tranche II Notes, each for cash, and Total purchasing $6.0 million of the Tranche II Notes through exchange and cancellation of the same amount of principal R&D Notes held by Total. As a result of the exchange and cancellation of the $6.0 million of R&D Note held by Total for the Tranche II Notes, the Company recorded a loss from extinguishment of debt of $9.4 million. The Tranche II Notes will be due sixty months from the date of issuance (January 15, 2019). Interest accrues on the Tranche II Notes at a rate per annum equal to 10%, compounded annually, and is payable in kind by adding to the principal every twelve months or in cash. Through June 30, 2017, the Company has elected to pay interest on the Tranche II Notes in kind.

The conversion price of the Tranche I Notes and Tranche II Notes is approximately $7.425 per share as of June 30, 2017.

As of June 30, 2017 and December 31, 2016, the related party convertible notes outstanding under the Tranche I Notes and Tranche II Notes were $22.1 million and $21.8 million, respectively, net of debt discount of $0.0 million and $0.0 million, respectively. Refer to the “Exchange” and “Maturity Treatment Agreement” sections of this Note 5, "Debt and Mezzanine Equity", for details of the impact of the Maturity Treatment and Exchange agreements on the Tranche I Notes and Tranche II Notes.

Loans Payable

In July 2012, the Company entered into a Note of Bank Credit and a Fiduciary Conveyance of Movable Goods Agreement (or, together, the July 2012 Bank Agreements) with each of Nossa Caixa Desenvolvimento (or Nossa Caixa) and Banco Pine S.A. (or Banco Pine). Under the July 2012 Bank Agreements, the Company pledged certain farnesene production assets as collateral for the loans of R$52.0 million (US$15.7 million based on the exchange rate as of June 30, 2017). The Company's total acquisition cost for such pledged assets was R$68.0 million (US$20.6 million based on the exchange rate as of June 30, 2017). The Company is also a parent guarantor for the payment of the outstanding balance under these loan agreements. Under the July 2012 Bank Agreements, the Company could borrow an aggregate of R$52.0 million (US$15.7 million based on the exchange rate as of June 30, 2017) as financing for capital expenditures relating to the Company's manufacturing facility located in Brotas, Brazil. The funds for the loans are provided by BNDES, but are guaranteed by the lenders. The loans have a final maturity date of July 15, 2022 and bear a fixed interest rate of 5.5% per year. The loans are also subject to early maturity and delinquency charges upon occurrence of certain events including interruption of manufacturing activities at the Company's manufacturing facility in Brotas, Brazil for more than 30 days, except during the sugarcane off-season. For the first two years that the loans were outstanding, the Company was required to pay interest only on a quarterly basis. Since August 15, 2014, the Company has been required to pay equal monthly installments of both principal and interest for the remainder of the term of the loans. As of June 30, 2017 and December 31, 2016, a principal amount of $10.0 million and $11.1 million, respectively, was outstanding under these loan agreements.

Exchange (Debt Conversion - Related Party Transaction)

In July 2015, the Company entered into an Exchange Agreement (or the "Exchange Agreement"), with Total and Temasek pursuant to which Temasek exchanged $71.0 million in principal amount of outstanding Tranche Notes (including paid-in-kind and accrued interest through July 29, 2015) and Total exchanged $70.0 million in principal amount of outstanding R&D Notes for shares of our common stock at a price of $34.50 per share (or the "Exchange"). As a result of the Exchange, accretion of debt discount was accelerated based on our estimate of the expected conversion date, resulting in an additional interest expense of $39.2 million for the year ended December 31, 2015.

Under the Exchange Agreement, Total also received the following warrants, each with a five-year term, at the closing of the Exchange:

The Temasek Exchange Warrant, the Temasek Funding Warrant and the Temasek R&D Warrant are referred to herein as the “Temasek Warrants” and the Temasek Warrants and the Total Warrants are hereinafter collectively referred to as the “Exchange Warrants”.

In addition to the grant of the Exchange Warrants, a warrant issued by the Company to Temasek in October 2013 in conjunction with a prior convertible debt financing (or the 2013 Warrant) became exercisable in full upon the completion of the Exchange. There were 66,667 shares underlying the 2013 Warrant, with an exercise price of $0.01 per share.

In February and May 2016, as a result of adjustments to the conversion price of the Tranche I Notes and Tranche II Notes (or, collectively, the Tranche Notes) discussed above, the Temasek Funding Warrant became exercisable for an additional aggregate of 164,169 shares of common stock. Following the issuance by the Company of shares of convertible preferred stock and warrants to purchase common stock in May 2017, as described below, and a corresponding adjustment to the conversion price of the Tranche I Notes and Tranche II Notes, as described above, the Temasek Funding Warrant became exercisable for an additional 1,125,755 shares of common stock.

As of March 1, 2017, the Company had not achieved the target cost per liter to manufacture farnesene provided in the Total R&D Warrant, and as a result, on March 1, 2017 the Total R&D Warrant became exercisable in accordance with its terms.

As of June 30, 2017, the Total Funding Warrant, the Temasek Exchange Warrant, and the 2013 Warrant had been fully exercised and Temasek had exercised the Temasek Funding Warrant with respect to 846,683 shares of common stock. Neither the Total R&D Warrant nor the Temasek R&D Warrant had been exercised as of June 30, 2017. Warrants to purchase 1,289,924 shares of common stock under the Temasek Funding Warrant were unexercised as of June 30, 2017. The exercise prices of the Exchange Warrants outstanding were $0.15 as of June 30, 2017.

Maturity Treatment Agreement

At the closing of the Exchange, the Company, Total and Temasek also entered into a Maturity Treatment Agreement, dated as of July 29, 2015, pursuant to which Total and Temasek agreed to convert any Tranche Notes or 2014 144A Notes held by them that were not canceled in the Exchange (or the Remaining Notes) into shares of the Company’s common stock in accordance with the terms of such Remaining Notes at or prior to maturity, provided that certain events of default had not occurred with respect to the applicable Remaining Notes. As of immediately following the closing of the Exchange, Temasek held $10.0 million in aggregate principal amount of Remaining Notes (consisting of 2014 144A Notes) and Total held $25.0 million in aggregate principal amount of Remaining Notes (consisting of $9.7 million of 2014 144A Notes and $15.3 million of Tranche Notes). In May 2017, the Company entered into separate letter agreements with each of Total and Temasek, pursuant to which the Company agreed that the Remaining Notes consisting of 2014 144A Notes held by Total and Temasek would no longer be subject to mandatory conversion at or prior to the maturity of such Remaining Notes. Accordingly, the Company will be required to pay any portion of such Remaining Notes that remain outstanding at maturity in cash in accordance with the terms of such Remaining Notes.

February 2016 Private Placement - Related Party Transaction

On February 12, 2016 and February 15, 2016, the Company issued and sold $18.0 million and $2.0 million, respectively, in aggregate principal amount of unsecured promissory notes (or the February 2016 Notes), as well as warrants to purchase 171,429 and 19,048 shares, respectively, of the Company’s common stock at an initial exercise price of $0.15 per share (or the February 2016 Warrants), representing aggregate proceeds to the Company of $20.0 million, in a private placement to certain existing stockholders of the Company that are affiliated with certain members of the Company’s Board of Directors: Foris Ventures, LLC (or Foris, an entity affiliated with director John Doerr of Kleiner Perkins Caufield & Byers, a current stockholder), which purchased $16.0 million aggregate principal amount of the February 2016 Notes and warrants to purchase 152,381 shares of the Company’s common stock; Naxyris S.A. (or Naxyris, an investment vehicle owned by Naxos Capital Partners SCA Sicar; director Carole Piwnica is Director of NAXOS UK, which is affiliated with Naxos Capital Partners SCA Sicar), which purchased $2.0 million aggregate principal amount of the February 2016 Notes and warrants to purchase 19,048 shares of the Company’s common stock; and Biolding Investment SA (or Biolding), a fund affiliated with director HH Sheikh Abdullah bin Khalifa Al Thani, which purchased $2.0 million aggregate principal amount of the February 2016 Notes and warrants to purchase 19,048 shares of the Company’s common stock.

The February 2016 Notes are unsecured obligations of the Company and are subordinate to the Company’s obligations under the Senior Secured Loan Facility pursuant to a Subordination Agreement, dated as of February 12, 2016, by and among the Company, the purchasers and the administrative agent under the Senior Secured Loan Facility. The February 2016 Notes bear interest at a rate of 13.50% per annum and had an initial maturity date of May 15, 2017. In May 2017, the February 2016 Notes purchased by Foris and Naxyris were exchanged for shares of preferred stock and warrants to purchase common stock, as described below, and in connection with such exchange the February 2016 Notes held by Foris and Naxyris were canceled. In addition, in May 2017, the Company and Biolding entered into a first amendment to the February 2016 Note held by Biolding (or the Biolding Note), pursuant to which the parties agreed to extend the maturity date of the Biolding Note from May 15, 2017 to November 15, 2017.

As of June 30, 2017, the February 2016 Warrants purchased by Naxyris had been fully exercised, while none of the February 2016 Warrants purchased by Foris or Biolding had been exercised. The exercise prices of the February 2016 Warrants were $0.15 per share as of June 30, 2017.

As of June 30, 2017, the carrying amount of the February 2016 Notes was $2.0 million.

June 2016 Private Placement - Related Party Transaction

On June 24, 2016, the Company issued and sold $5.0 million in aggregate principal amount of secured promissory notes (or the June 2016 Notes) to Foris in a private placement. The interest rate on the June 2016 Notes was 13.50% per annum and the June 2016 Notes had a maturity date of May 15, 2017. In May 2017, the June 2016 Notes were exchanged for shares of preferred stock and warrants to purchase common stock, as described below, and in connection with such exchange the June 2016 Notes were canceled and the agreements relating thereto (including the security interest relating thereto) were terminated.

October 2016 Private Placements

On October 21 and October 27, 2016, the Company issued and sold $6.0 million and $8.5 million, respectively, in aggregate principal amount of secured promissory notes (or the October 2016 Notes) to Foris and Ginkgo, respectively in private placements (or the October 2016 Private Placements). The interest rate on the October 2016 Notes was 13.50% per annum and the October 2016 Notes had a maturity date of May 15, 2017. In May 2017, the October 2016 Notes purchased by Foris were exchanged for shares of preferred stock and warrants to purchase common stock, as described below, and in connection with such exchange the October 2016 Notes purchased by Foris were canceled and the agreements relating thereto (including the security interest relating thereto) were terminated. The October 2016 Notes purchased by Ginkgo were repaid in full at maturity in May 2017, and the agreements relating thereto (including the security interest relating thereto) were terminated.

Salisbury Note

In December 2016, in connection with the Company’s purchase of a manufacturing facility in Leland, North Carolina and related assets (or the Glycotech Assets), the Company issued a purchase money promissory note in the principal amount of $3.5 million (or the Salisbury Note) in favor of Salisbury Partners, LLC. The Salisbury Note (i) bore interest at a rate of 5% per year, (ii) had a term of 13 years, (iii) was payable in equal monthly installments of principal and interest beginning on January 1, 2017 (which payments would be subject to a penalty of 5% if delinquent more than 5 days) and (iv) was secured by a purchase money lien on the Glycotech Assets. In January 2017, the Salisbury Note was repaid with proceeds from the Nikko Note (as defined below) and the agreements relating thereto (including the security interest relating thereto) were terminated.

Nikko Note

In December 2016, in connection with the Company’s formation of its cosmetics joint venture (or the Aprinnova JV) with Nikko Chemicals Co., Ltd. (or Nikko), an existing commercial partner of the Company, and Nippon Surfactant Industries Co., Ltd., an affiliate of Nikko, as discussed in Note 7, “Joint Venture and Noncontrolling Interests,” Nikko made a loan to the Company in the principal amount of $3.9 million, and the Company in consideration therefor issued a promissory note (or the Nikko Note) to Nikko in an equal principal amount. The proceeds of the Nikko Note were used to satisfy the Company’s remaining liabilities relating to the Company’s purchase of the Glycotech Assets, including liabilities under the Salisbury Note. The Nikko Note (i) bears interest at a rate of 5% per year, (ii) has a term of 13 years, (iii) is payable in equal monthly installments of principal and interest beginning on January 1, 2017 (which payments are subject to a penalty of 5% if delinquent more than 5 days) and (iv) is collateralized by a first-priority lien on 10% of the Aprinnova JV interests owned by the Company. In addition to the payments under the Nikko Note set forth in the preceding sentence, the Company is required to (i) repay $400,000 of the Nikko Note in equal monthly installments of $100,000 on January 1, 2017, February 1, 2017, March 1, 2017 and April 1, 2017 and (ii) commencing with the distributions from the Aprinnova JV to its members relating to the fourth fiscal year of the Aprinnova JV and continuing for each fiscal year thereafter until the Nikko Note is fully repaid, repay the Nikko Note in an amount equal to the profits, if any, distributed to the Company by the Aprinnova JV. The Nikko Note may be prepaid in full or in part at any time without penalty or premium.

Future minimum payments under the debt agreements as of June 30, 2017 are as follows (in thousands):

(1) includes debt discount & issuance cost associated with related party & non-related party debt which will accrete to interest expense under the effective interest method over the term of the debt.

Bill & Melinda Gates Foundation Investment (Mezzanine Equity)

On May 10, 2016, the Company issued and sold 292,398 shares of common stock at a purchase price per share equal to approximately $17.10 to the Bill & Melinda Gates Foundation (or the Gates Foundation) in a private placement, resulting in aggregate proceeds to the Company of $5.0 million (or the Gates Foundation Investment). In connection with the Gates Foundation Investment, the Company and the Gates Foundation entered into a Charitable Purposes Letter Agreement, pursuant to which the Company agreed to expend an aggregate amount not less than the amount of the Gates Foundation Investment to develop a yeast strain that produces artemisinic acid and/or amorphadiene at a low cost and to supply such artemisinic acid and amorphadiene to companies qualified to convert artemisinic acid and amorphadiene to artemisinin for inclusion in artemisinin combination therapies used to treat malaria commencing in 2017. If the Company defaults in its obligation to use the proceeds from the Gates Foundation Investment as set forth above or defaults under certain other commitments in the Charitable Purposes Letter Agreement, the Gates Foundation will have the right to request that the Company redeem, or facilitate the purchase by a third party of, the Gates Foundation Investment shares then held by the Gates Foundation at a price per share equal to the greater of (i) the closing price of the Company’s common stock on the trading day prior to the redemption or purchase, as applicable, and (ii) the per share price paid by the Gates Foundation for the Gates Foundation Investment shares plus a compounded annual return of 10%. As of June 30, 2017, $5.0 million of the funding received was classified as mezzanine equity. The Company continues to meet its obligation to use the proceeds as set forth above and believes it will continue to do so. The probability of default is low resulting in the equity instrument not being adjusted to its redemption amount.

May 2017 Financing Transactions

On May 8, 2017 and May 31, 2017, the Company entered into separate Securities Purchase Agreements (or the May 2017 Purchase Agreements) with certain investors for the issuance and sale of an aggregate of 22,140 shares of the Company’s Series A 17.38% Convertible Preferred Stock, par value $0.0001 per share (or the Series A Preferred Stock), 70,904 shares of the Company’s Series B 17.38% Convertible Preferred Stock, par value $0.0001 per share (or the Series B Preferred Stock and, together with the Series A Preferred Stock, the Preferred Stock), which Preferred Stock is convertible into the Company’s common stock, par value $0.0001 per share as described below, and Cash Warrants (as defined below) to purchase an aggregate of 14,768,380 shares of common stock and Dilution Warrants (as defined below) (or, collectively, the May 2017 Warrants, and the shares of common stock issuable upon exercise of the Warrants, the May 2017 Warrant Shares) (or the May 2017 Offerings).

The May 2017 Offerings closed on May 11, 2017 (or the May 11 Offering) and May 31, 2017, respectively. The net proceeds to the Company from the May 2017 Offerings were $50.2 million after payment of offering expenses and placement agent fees. The Series A Preferred Stock and May 2017 Warrants relating thereto were sold to the purchasers thereof in exchange for aggregate cash consideration of $22,140,000, and the Series B Preferred Stock and May 2017 Warrants relating thereto were sold to the purchasers thereof in exchange for (i) aggregate cash consideration of $30,700,000 and (ii) the cancellation of $40.2 million of outstanding indebtedness and including accrued interest thereon, owed by the Company to such purchasers, of which $33.1 million was from related parties, as further described below.

The May 2017 Purchase Agreements include customary representations, warranties and covenants of the parties. In addition, pursuant to the May 2017 Purchase Agreements, the Company, subject to certain exceptions, including the issuance of the Second Tranche Securities (as defined below), (i) may not issue, enter into any agreement to issue or announce the issuance or proposed issuance of any shares of Common Stock or securities convertible into or exercisable or exchangeable for common stock until July 31, 2017 and (ii) may not enter into an agreement to effect any issuance by the Company involving a variable rate transaction until one year from the closing of the May 11 Offering.

Series A Preferred Stock (Permanent Equity)

Each share of Series A Preferred Stock has a stated value of $1,000 and is convertible at any time, at the option of the holder, into common stock at conversion price of $17.25 per share (or the Preferred Stock Conversion Rate). The Preferred Stock Conversion Rate is subject to adjustment in the event of any dividends or distributions of common stock, or any stock split, reverse stock split, recapitalization, reorganization or similar transaction. If not previously converted at the option of the holder, each share of Series A Preferred Stock will be automatically converted, without any further action by the holder, on October 9, 2017, the 90th day following the date that the Stockholder Approval (as defined below) was obtained and effected.

Dividends, at a rate per year equal to 17.38% of the stated value of the Series A Preferred Stock, will be payable semi-annually from the issuance of the Series A Preferred Stock until the tenth anniversary of the date of issuance, on each October 15 and April 15, beginning October 15, 2017, on a cumulative basis, at the Company’s option, in cash, out of any funds legally available for the payment of dividends, or, subject to the satisfaction of certain conditions, in Common Stock at the Preferred Stock Conversion Rate, or a combination thereof. In addition, upon the conversion of the Series A Preferred Stock prior to the tenth anniversary of the date of issuance, the holders of the Series Preferred A Stock shall be entitled to a payment equal to $1,738 per $1,000 of stated value of the Series A Preferred Stock, less the amount of all prior semi-annual dividends paid on such converted Series A Preferred Stock prior to the relevant conversion date (the Preferred Stock Make-Whole Payment), at the Company’s option, in cash, out of any funds legally available for the payment of dividends, or, subject to the satisfaction of certain conditions, in Common Stock at the Preferred Stock Conversion Rate, or a combination thereof. If the Company elects to pay any dividend in the form of cash, it shall provide each holder with notice of such election not later than the first day of the month of prior to the applicable dividend payment date.

Unless and until converted into common stock in accordance with its terms, the Series A Preferred Stock has no voting rights, other than as required by law or with respect to matters specifically affecting the Series A Preferred Stock.

In the event of a fundamental transaction, the holders of the Series A Preferred Stock will have the right to receive the consideration receivable as a result of such fundamental transaction by a holder of the number of shares of Common Stock for which the Series A Preferred Stock is convertible immediately prior to such fundamental transaction (without regard to whether such Series A Preferred Stock is convertible at such time), which amount shall be paid pari passu with all holders of Common Stock.

Upon any liquidation, dissolution or winding-up of the Company, the holders of the Series A Preferred Stock shall be entitled to receive out of the assets of the Company the same amount that a holder of Common Stock would receive if the Series A Preferred Stock were fully converted to Common Stock immediately prior to such liquidation, dissolution or winding-up (without regard to whether such Series A Preferred Stock is convertible at such time), which amount shall be paid pari passu with all holders of Common Stock.

Notwithstanding the foregoing, the holders (other than the Designated Holder (as defined below)) will not have the right to convert any Series A Preferred Stock, and the Company shall not effect any conversion of the Series A Preferred Stock, if the holder, together with its affiliates, would beneficially own in excess of 4.99% (or such other percentage as determined by the holder and notified to the Company in writing, not to exceed 9.99%, provided that any increase of such percentage will not be effective until 61 days after notice thereof) of the number of shares of common stock outstanding immediately after giving effect to the issuance of shares of common stock issuable upon conversion of such Series A Preferred Stock (or the Beneficial Ownership Limitation).

The Series A Preferred Stock were offered and sold pursuant to a prospectus filed with the SEC on April 9, 2015 and a prospectus supplement dated May 8, 2017, in connection with a takedown from the Company’s effective shelf registration statement on Form S-3 (File No. 333-203216) declared effective by the SEC on April 15, 2015.

On May 8, 2017, the Company filed the Certificate of Designation of Preferences, Rights and Limitations of Series A 17.38% Convertible Preferred Stock with the Secretary of State of Delaware.

The Series A preferred stock has been classified as permanent equity, as the Company controls all actions or events required to settle the Optional and Mandatory Conversion feature in shares. The make whole payment was determined to be an embedded derivative requiring bifurcation and separate recognition as a derivative liability recognized at its fair value as of the issuance date with subsequent changes in fair value recorded in earnings until the Series A preferred stock is converted into common stock and the make whole payment is paid or until the make whole payment is paid through declared dividends or cash. The Series A preferred stock also contains a beneficial conversion feature which has been recognized up to the amount of proceeds allocated to the preferred stock ($0.6 million). Subsequent to the recognition of the beneficial conversion feature, the net proceeds allocated to the Series A preferred stock was $0.0 million.

As of June 30, 2017, 18,840 shares of Series A preferred stock had converted into common stock, resulting in the recognition of a gain in the change in fair value of derivative liabilities of $9.4 million.

Series B Preferred Stock (Mezzanine Equity)

The Series B Preferred Stock has substantially identical terms to the Series A Preferred Stock (as described above), except that the issuance of the shares of common stock issuable upon conversion of the Series B Preferred Stock or as payment of dividends or the Make-Whole Payment on the Series B Preferred Stock (or the Series B Conversion Shares) was initially subject to the Stockholder Approval (as defined below).

The Series B Preferred Stock was accounted for as Mezzanine equity as the embedded conversion options are not able to be settled in shares under circumstances within the Company’s control.

The investors of the Series B Preferred Stock included related parties affiliated with certain members of the Company’s Board of Directors (or the Affiliated Investors). Foris exchanged an aggregate principal amount of $27.0 million of indebtedness, plus accrued interest thereon, issued to Foris by the Company on February 12, 2016, June 24, 2016 and October 21, 2016, as described above, for 30,728.589 shares of Series B Preferred Stock and May 2017 Warrants to purchase 4,877,386 shares of Common Stock. Naxyris exchanged an aggregate principal amount of $2.0 million of indebtedness, plus accrued interest thereon, issued to Naxyris by the Company on February 15, 2016, as described above, for 2,333.216 shares of Series B Preferred Stock and May 2017 Warrants to purchase 370,404 shares of common stock. The fair value of the Series B preferred stock, embedded make whole payment and related warrants exceeded the carrying value of the related party debt and accrued interest exchanged by $8.6 million which has been recorded as a reduction to Additional Paid in Capital and considered a deemed dividend, increasing net loss attributable to Amyris, Inc. common stockholders.

Certain investors of the Series B Preferred Stock included holders of certain of the Company’s existing indebtedness, including the 2014 144A Notes and the 2015 144A Notes. These investors exchanged all or a portion of their holding of such indebtedness, including accrued interest thereon, representing an aggregate of $3.4 million of 2014 144A Notes and $3.7 million of 2015 144A Notes, for Series B Preferred Stock and May 2017 Warrants in the May 2017 Offering. Upon the closing of the May 11 Offering, such indebtedness was canceled and the agreements relating thereto, including any note purchase agreements or unsecured or secured promissory notes (including any security interest relating thereto), were terminated, except to the extent such investors or other investors retain a portion of such indebtedness. The fair value of the Series B preferred stock, embedded make whole payment and related warrants exceeded the carrying value of the debt and accrued interest exchanged by $1.9 million which has been recognized as a loss on extinguishment of debt in other income (expense).

The remaining Series B preferred stock was purchased in exchange for cash proceeds of $30.7 million. The Series B preferred stock issued to the Designated Holder contains a contingent beneficial conversion feature that will be recognized when Stockholder Approval has been obtained and the conversion is no longer contingent. The conversion feature (the right to negotiate the Second Tranche Funding Option) is not a separate unit of account requiring bifurcation.

A derivative liability has been recognized at fair value on the date of issuance for the make whole payment in the amount of $34.7 million. Changes in the fair value of this derivative from the date of issuance through June 30, 2017 have been recorded in earnings. Issuance costs of $0.8 million have been recognized in Sales, General and Administrative expenses.

May 2017 Warrants

Pursuant to the May 2017 Purchase Agreements, the Company issued to each investor (i) a warrant, with an exercise price of $7.80 per share as of June 30, 2017, to purchase a number of shares of Common Stock equal to 50% of the shares of common stock into which such investor’s shares of Preferred Stock were initially convertible (including shares of common stock issuable as payment of the Make-Whole Payment, assuming that the Make-Whole Payment is made in common stock), representing warrants to purchase 7,384,190 shares of common stock in the aggregate for all investors and (ii) a warrant, with an exercise price of $9.30 per share as of June 30, 2017, to purchase an equal number of shares of common stock, representing warrants to purchase 7,384,190 shares of common stock in the aggregate for all investors (or, collectively, the Cash Warrants). The exercise price of the Cash Warrants is subject to standard adjustments as well as full-ratchet anti-dilution protection for any issuance by the Company of equity or equity-linked securities during the three-year period following the issuance of such Cash Warrants at a per share price (including any conversion or exercise price, if applicable) less than the then-current exercise price of the Cash Warrants, subject to certain exceptions.

In addition, the Company issued to each investor a warrant, with an exercise price of $0.0015 per share as of June 30, 2017 (or, collectively, the Dilution Warrants), to purchase a number of shares of common stock sufficient to provide the investor with full-ratchet anti-dilution protection for any issuance by the Company of equity or equity-linked securities during the three-year period following the issuance of the Dilution Warrants at a per share price (including any conversion or exercise price, if applicable) less than $6.30 per share, the effective per share price paid by the investors for the shares of common stock issuable upon conversion of the Preferred Stock purchased by the investors in the May 2017 Offerings (including shares of common stock issuable as payment of dividends or the Make-Whole Payment, assuming that all such dividends and the Make-Whole Payment are made in common stock), subject to certain exceptions.

The exercise of the May 2017 Warrants was subject to the Stockholder Approval (as defined below). The May 2017 Warrants each have a term of five years from the date such warrants are initially exercisable. The exercise of the May 2017 Warrants is subject to the Beneficial Ownership Limitation.

The Cash Warrants are freestanding financial instruments that are accounted for as derivative liabilities and recognized at their fair value on the date of issuance of $39.5 million. Subsequent changes to their fair value will be recorded in earnings until the warrants are exercised or expire in May 2022.

The full-ratchet anti-dilution protection of the Cash Warrants are also freestanding financial instruments that have been accounted for as derivative liabilities and recognized at their fair value on the date of issuance of $4.4 million. Subsequent changes to their fair value will be recorded in earnings until they are exercised or expire in May 2020.

Stockholder Approval

Pursuant to the May 2017 Purchase Agreements, the Company agreed to solicit from the Company’s stockholders (i) any approval for the transactions contemplated by the May 2017 Purchase Agreement required by the rules and regulations of the NASDAQ Stock Market, including without limitation the issuance of shares of common stock upon conversion of the Series B Preferred Stock and upon exercise of the May 2017 Warrants (or the NASDAQ Approval) and (ii) approval to effect a reverse stock split of the common stock (together with the NASDAQ Approval, collectively, the Stockholder Approval) at an annual or special meeting of stockholders to be held on or prior to July 10, 2017, and to use commercially reasonable efforts to secure the Stockholder Approval. The Stockholder Approval was obtained on July 7, 2017.

Registration Rights

Pursuant to the May 2017 Purchase Agreements, within 30 calendar days of the date of the Stockholder Approval, the Company has agreed to file a registration statement on Form S-3 (or other appropriate form if the Company is not then S-3 eligible) providing for the resale by the investors of the Series B Conversion Shares and May 2017 Warrant Shares. The Company has also agreed to use commercially reasonable efforts to cause such registration statement to become effective within 181 days following the Closing and commercially reasonable efforts to keep such registration statement effective at all times until (i) no Investor owns any Series B Conversion Shares or May 2017 Warrant Shares or (ii) the Series B Conversion Shares and May 2017 Warrant Shares are eligible for resale under Rule 144 without regard to volume limitations. On August [4], 2017, the Company filed a registration statement on Form S-3 with the SEC to register the Series B Conversion Shares and May 2017 Warrant Shares for resale by the investors in accordance with the May 2017 Purchase Agreements.

Stockholder Agreement

In connection with the May 2017 Purchase Agreements, on May 11, 2017, the Company and one of the investors, DSM International B.V. (or the Designated Holder), a subsidiary of Koninklijke DSM N.V., entered into a Stockholder Agreement (or the Stockholder Agreement) setting forth certain rights and obligations of the Designated Holder and the Company. The Designated Holder purchased 25,000 shares of Series B Preferred Stock, Cash Warrants for the purchase of 3,968,116 shares of Common Stock and Dilution Warrants in the May 2017 Offering in exchange for aggregate cash consideration of $25,000,000. Pursuant to the Stockholder Agreement, the Designated Holder has the right to designate one director selected by the Designated Holder (or a Designated Holder Director), subject to certain restrictions, to the Company’s Board of Directors (or the Board). The Company agreed to appoint the Designated Holder Director, such appointment occurring on May 18, 2017, and to use reasonable efforts, consistent with the Board’s fiduciary duties, to cause the Designated Holder Director to be re-nominated in the future; provided, that the Designated Holder will no longer have the right to designate any Designated Holder Director at such time as the Designated Holder holds less than 4.5% of the Company’s outstanding common stock. In addition, for as long as there is a Designated Holder Director serving on the Board, the Company agreed not to engage in certain commercial or financial transactions or arrangements without the consent of any then-serving Designated Holder Director. The Company also agreed to provide the Designated Holder with certain exclusive negotiating rights in connection with certain future commercial projects and arrangements, whereby the Designated Holder will have a 60-day negotiation period with respect to any such projects, as well as a right to use a portion of the Company’s manufacturing capacity for toll manufacturing of the Designated Holder’s products, subject to certain conditions, including, with respect to the toll manufacturing option, that the Designated Holder provide the Company with a minimum annual level of cash funding in connection with commercial activity between the Company and the Designated Holder, beginning in 2018. The Designated Holder will have the right to purchase additional shares of capital stock of the Company in connection with a sale of equity or equity-linked securities by the Company in a capital raising transaction for cash, subject to certain exceptions, to maintain its proportionate ownership percentage in the Company. In connection with the Stockholder Agreement, the Company and the Designated Holder entered into licenses granted by the Company to the Designated Holder with respect to certain Company intellectual property useful in the Designated Holder’s business (or the License Agreements), which licenses will become effective upon the occurrence of certain events specified therein.

Pursuant to the Stockholder Agreement, the Designated Holder agreed not to sell or transfer any of the shares of Series B Preferred Stock or May 2017 Warrants purchased by the Designated Holder in the May 2017 Offerings, any Second Tranche Securities (as defined below), or any shares of common stock issuable upon conversion or exercise thereof (or the Transfer Restricted Shares), other than to its affiliates, without the consent of the Company during the one-year period following the entry into the Stockholder Agreement. Thereafter, the Designated Holder will have the right to sell or transfer the Transfer Restricted Shares to any third party, other than a competitor of the Company or any controlled affiliate of a competitor of the Company; provided, that the Company will have a customary right of first offer with respect to any such sale or transfer other than to affiliates of the Designated Holder. In addition, the Designated Holder agreed that, other than in connection with the purchase, conversion or exercise of (i) the Series B Preferred Stock or May 2017 Warrants purchased by the Designated Holder pursuant to the May 2017 Purchase Agreement or (ii) the Second Tranche Securities (as defined below) in accordance with their terms or the exercise of its pre-emptive rights, until three months after there is no Designated Holder Director on the Board, the Designated Holder will not, without the prior consent of the Board, among other things, purchase any Common Stock, any options or other rights to acquire Common Stock or any indebtedness of the Company, or make any public offer to acquire common stock, options or other rights to acquire common stock or indebtedness of the Company, that would result in the Designated Holder and its affiliates beneficially owning more than 33% of the Company’s outstanding voting securities at the time of acquisition (assuming the exercise or conversion, whether then exercisable or convertible, of any shares of Series B Preferred Stock, May 2017 Warrants or Second Tranche Securities beneficially owned by the Designated Holder and/or its affiliates), join in any solicitation of proxies for any matter not previously approved by the Board, or join any “group” (as such term is defined in Section 13(d)(3) of the Securities Exchange Act of 1934) with respect to any of the foregoing.

Pursuant to the Stockholder Agreement, the Company and the Designated Holder agreed to negotiate in good faith during the 90-day period following the entry into the Stockholder Agreement to mutually agree on certain terms and conditions upon which the Designated Holder shall purchase additional shares of Series B Preferred Stock and warrants (or the Second Tranche Securities), in an amount to be agreed by the Company and the Designated Holder, provided such amount is no less than $25 million and no more than $30 million (such amount, the Second Tranche Funding Amount) prior to the end of such 90-day period (or the Second Tranche Funding). The Second Tranche Funding is subject to approval of the Designated Holder’s managing board. In connection with the Second Tranche Funding, the Company and the Designated Holder shall enter into an amendment to the Stockholder Agreement providing for a second Designated Holder Director on terms to be agreed by the parties, and certain of the License Agreements will become effective. If the Second Tranche Funding occurs, the parties will thereafter negotiate in good faith regarding an agreement concerning the development of certain products in the health and nutrition field. In the event that the parties do not reach such agreement prior to the earlier of 90 days after the Second Tranche Funding or December 31, 2017, (a) the exclusive negotiating right granted to the Designated Holder in connection with certain future commercial projects and arrangements of the Company will expire, (b) on the first anniversary of the closing of the Second Tranche Funding and each subsequent anniversary thereof, the Company will make a $5 million cash payment to the Designated Holder, provided that the aggregate amount of such payments shall not exceed the Second Tranche Funding Amount, and (c) an intellectual property escrow agreement relating to the License Agreements, entered into by the Company and the Designated Holder upon the entry into the Stockholder Agreement, will become effective. See Note 14, “Subsequent Events”, for more details regarding the Second Tranche Funding.

Series C Preferred Stock

Exchange

In connection with the transactions contemplated by the May 2017 Purchase Agreements, on May 8, 2017, the Company entered into a Security Holder Agreement with Foris and Naxyris. Pursuant to the Security Holder Agreement, Foris and Naxyris agreed to exchange (or the May 2017 Exchange) their outstanding shares of common stock, representing a total of 1,394,706 shares, for 20,921 shares of the Company’s Series C Convertible Preferred Stock, par value $0.0001 per share (or the Series C Preferred Stock). In addition, pursuant to the Security Holder Agreement, Foris and Naxyris agreed to not convert any of their outstanding convertible promissory notes, warrants or any other equity-linked securities of the Company until the Stockholder Approval. The May 2017 Exchange was consummated on May 11, 2017.

Each share of Series C Preferred Stock has a stated value of $1,000 and automatically converts into common stock, at a conversion price of $15 per share (or the Series C Conversion Rate), upon the approval by the Company’s stockholders and implementation of the reverse stock split. The Series C Conversion Rate is subject to adjustment in the event of any dividends or distributions of the common stock, or any stock split, reverse stock split, recapitalization, reorganization or similar transaction.

The Series C Preferred Stock is entitled to participate with the common stock on an as-converted basis with respect to any dividends or other distributions to holders of common stock.

The Series C Preferred Stock shall vote together as one class with the common stock on an as-converted basis, and shall also vote with respect to matters specifically affecting the Series C Preferred Stock.

In the event of a fundamental transaction, the holders of the Series C Preferred Stock will have the right to receive the consideration receivable as a result of such fundamental transaction by a holder of the number of shares of common stock for which the Series C Preferred Stock is convertible immediately prior to such fundamental transaction (without regard to whether such Series C Preferred Stock is convertible at such time), which amount shall be paid pari passu with all holders of common stock.

Upon any liquidation, dissolution or winding-up of the Company, the holders of the Series C Preferred stock shall be entitled to receive out of the assets of the Company an amount equal to the greater of (i) the par value of each share of Series C Preferred Stock, plus any accrued and unpaid dividends or other amounts due on such Series C Preferred Stock, prior to any distribution or payment to the holders of common stock or (ii) the amount that a holder would receive if the Series C Preferred Stock were fully converted to common stock immediately prior to such liquidation, dissolution or winding-up (without regard to whether such Series C Preferred Stock is convertible at such time), which amount shall be paid pari passu with all holders of Common Stock.

The shares of Series C Preferred Stock automatically converted to common stock on June 6, 2017 as a result of the 15:1 reverse stock split becoming effective. The Company accounted for the Series C Preferred Stock as a non-monetary transaction that had no impact on the interim financial statements.

6. Commitments and Contingencies

Lease Obligations

The Company leases certain facilities and finances certain equipment under operating and capital leases, respectively. Operating leases include leased facilities and capital leases include leased equipment (see Note 4, "Balance Sheet Components"). The Company recognizes rent expense on a straight-line basis over the noncancelable lease term and records the difference between rent payments and the recognition of rent expense as a deferred rent liability. Where leases contain escalation clauses, rent abatements, and/or concessions, such as rent holidays and landlord or tenant incentives or allowances, the Company applies them as a straight-line rent expense over the lease term. The Company has noncancelable operating lease agreements for office, research and development, and manufacturing space, and equipment, that expire at various dates, with the latest expiration in February 2031. Rent expense under operating leases was $1.4 million and $1.4 million for the three months ended June 30, 2017 and 2016, respectively, and $2.8 million and $2.7 million for the six months ended June 30, 2017 and 2016, respectively.

Future minimum payments under the Company's lease obligations as of June 30, 2017 are as follows (in thousands):

Guarantor Arrangements

The Company has agreements whereby it indemnifies its officers and directors for certain events or occurrences while the officers or directors are serving in their official capacities. The indemnification period remains enforceable for the officer's or director’s lifetime. The maximum potential amount of future payments the Company could be required to make under these indemnification agreements is unlimited; however, the Company has a director and officer insurance policy that limits its exposure and enables the Company to recover a portion of any future payments. As a result of its insurance policy coverage, the Company believes the estimated fair value of these indemnification agreements is minimal. Accordingly, the Company had no liabilities recorded for these agreements as of June 30, 2017 and December 31, 2016.

Purchase Obligations

As of June 30, 2017 and December 31, 2016, the Company had $0.9 million and $0.8 million, respectively, in purchase obligations which included $0.6 million and $0.6 million, respectively, of noncancelable contractual obligations and construction commitments.

Production Cost Commitment

As of June 30, 2017, the Company was committed to manufacture and supply squalane and hemisqualane to the Aprinnova JV at specified cost targets. The Company is obligated to pay all manufacturing costs above the production cost target but is not obligated to produce squalane and hemisqualane at a loss. The Company’s obligations under this arrangement for the three and six months ended June 30, 2017 were offset by its entitlement to all of the profits of the Aprinnova JV for the periods, which entitlement continues for the three year period following the date of the Joint Venture Agreement relating to the Aprinnova JV, up to a maximum of $10 million.

Other Matters

Certain conditions may exist as of the date the financial statements are issued, which may result in a loss to the Company but will only be recorded when one or more future events occur or fail to occur. The Company's management assesses such contingent liabilities, and such assessment inherently involves an exercise of judgment. In assessing loss contingencies related to legal proceedings that are pending against and by the Company or unasserted claims that may result in such proceedings, the Company's management evaluates the perceived merits of any legal proceedings or unasserted claims as well as the perceived merits of the amount of relief sought or expected to be sought.

If the assessment of a contingency indicates that it is probable that a material loss has been incurred and the amount of the liability can be estimated, then the estimated liability would be accrued in the Company's financial statements. If the assessment indicates that a potential material loss contingency is not probable but is reasonably possible, or is probable but cannot be reasonably estimated, then the nature of the contingent liability, together with an estimate of the range of possible loss if determinable and material would be disclosed. Loss contingencies considered to be remote by management are generally not disclosed unless they involve guarantees, in which case the guarantee would be disclosed.

The Company has levied indirect taxes on sugarcane-based biodiesel sales by Amyris Brasil to customers in Brazil based on advice from external legal counsel. In the absence of definitive rulings from the Brazilian tax authorities on the appropriate indirect tax rate to be applied to such product sales, the actual indirect rate to be applied to such sales could differ from the rate we levied.

In April 2017, a securities class action complaint was filed against Amyris and our CEO, John G. Melo, and CFO, Kathleen Valiasek, in the U.S. District Court for the Northern District of California. The complaint seeks unspecified damages on behalf of a purported class that would comprise all individuals who acquired our common stock between March 2, 2017 and April 17, 2017. The complaint alleges securities law violations based on statements made by the Company in its earnings press release issued on March 2, 2017 and Form 12b-25 filed with the SEC on April 3, 2017. We believe the complaint lacks merit, and intend to defend ourselves vigorously.

In June 2017, an alleged shareholder, Pedro Gutierrez, caused a purported shareholder derivative suit entitled Gutierrez v John G. Melo et al , Case No. BC 665782, to be filed in the Superior Court for the State of California, County of Los Angeles. The lawsuit names Amyris Inc. as a nominal defendant and names a number of the Company's current officers and directors as additional defendants. The lawsuit seeks to recover, on the Company's behalf, unspecified damages purportedly sustained by the Company in connection with allegedly misleading statements and/or omissions made in connection with the Company's securities filings. It also seeks a series of changes to the Company's corporate governance policies, restitution to the Company from the individual defendants, and an award of attorneys' fees. This purported shareholder derivative action is based on substantially the same facts as the securities class action described above. We do not believe the claims in the complaint have merit, and intend to defend ourselves vigorously.

The Company is subject to disputes and claims that arise or have arisen in the ordinary course of business and that have not resulted in legal proceedings or have not been fully adjudicated. Such matters that may arise in the ordinary course of business are subject to many uncertainties and outcomes are not predictable with reasonable assurance and therefore an estimate of all the reasonably possible losses cannot be determined at this time. Therefore, if one or more of these legal disputes or claims resulted in settlements or legal proceedings that were resolved against the Company for amounts in excess of management’s expectations, the Company’s condensed consolidated financial statements for the relevant reporting period could be materially adversely affected.

In September 2014, the Company entered into a supply agreement with Firmenich for compounds developed under the Firmenich Collaboration Agreement. The Company recognized $0.9 million and $2.6 million of revenues from product sales under this agreement for the three months ended June 30, 2017 and 2016, respectively and $2.1 million and $4.6 million for the six months ended June 30, 2017 and 2016, respectively.

In December 2016, the Company and Firmenich entered into an amendment of the Firmenich Collaboration Agreement, pursuant to which the parties agreed to exclude certain compounds from the scope of the agreement and to permit the Company to engage in certain activities relating to such excluded compounds with a third party, in exchange for a ten percent royalty on net sales by the Company to such third party of products related to such excluded compounds, as well as (i) the transfer of certain technical materials relating to the Firmenich Collaboration Agreement, previously held in escrow, to Firmenich, (ii) a credit to Firmenich against products previously ordered from the Company under the parties’ existing supply agreement, (iii) a reduced price for the sale of additional products to Firmenich under such supply agreement, and (iv) training for the employees of Firmenich at the Company’s manufacturing plant located in Brotas, Brazil. As a result of the 2016 amendment, the Company's arrangements are considered for revenue recognition purposes to comprise a single multiple-element arrangement.

Kuraray Collaboration Agreement

In July 2011, the Company entered into a collaboration agreement with Kuraray Co., Ltd (or Kuraray), with an initial focus on using farnesene-based polymers to replace petroleum-derived additives in tires. In March 2014, the Company entered into the Second Amended and Restated Collaboration Agreement with Kuraray in order to extend the term of the original collaboration agreement between the Company and Kuraray for an additional two years and add additional fields and products to the scope of development. In consideration for the Company’s agreement to extend the term of the original collaboration agreement and add additional fields and products, Kuraray agreed to pay the Company $4.0 million in two equal installments of $2.0 million. The first installment was paid on April 30, 2014 and the second installment was due on April 30, 2015. In March 2015, the Company and Kuraray entered into the First Amendment to the Second Amended and Restated Collaboration Agreement to extend the term of the collaboration agreement until December 31, 2016 and to accelerate payment to the Company of the second installment of $2.0 million due from Kuraray under the Second Amended and Restated Collaboration Agreement to March 31, 2015. Subsequently, in November 2016 the Company and Kuraray entered into Amendment #3 to the Second Amended and Restated Collaboration Agreement to, among other things, extend the term of the collaboration agreement to December 31, 2018 as well as extend certain exclusive rights granted to Kuraray under the collaboration agreement. In connection with such extensions, Kuraray agreed to pay the Company $1.0 million in two equal installments of $500,000 on or before January 15, 2017 and January 15, 2018, respectively.

Under this agreement, the Company recognized (i) collaboration revenues of $0.1 million and $0.4 million for the three months ended June 30, 2017 and 2016, respectively, and $0.3 million and $0.8 million for the six months ended June 30, 2017 and 2016, respectively, and (ii) revenues from product sales of $1.9 million and $0.2 million for the three months ended June 30, 2017 and 2016, respectively, and $3.6 million and $0.2 million for the six months ended June 30, 2017 and 2016, respectively.