Automated Synthesis Facility

La Jolla, California Campus

The Automated Synthesis Facility provides hardware, software, and services in support of data-rich synthetic experiments. The facility helps synthetic chemists with all phases of a project, including project planning, reaction setup, reaction analysis, product purification, and data visualization. The staff assist users with developing project-specific instrument protocols and custom data processing and reporting. Projects of all sizes are welcome.

9:00 a.m. - 6:00 p.m. (PT) or by appointment

Equipment for reaction setup:

  • Unchained Labs Freeslate robotic platform with liquid handling, solid dispense, mixing, temperature control, filtration, and pressure capabilities, housed in a nitrogen purge box
  • Unchained Labs Freeslate Jr with OSR robotic platform with parallel pressure reactors with overhead stirring, independent temperature control, independent pressure control, and the ability to add reagents and remove reaction aliquots while under pressure, housed in a nitrogen purge box
  • ThermoFisher plate SpeedVac, housed in the same nitrogen purge box as the Freeslate robotic platform
  • V&P Scientific tumble stirrer with independent heating zones, not in purge box

ASF Lab 1

Equipment for analysis:

  • Waters I-Class LC with diode array and G2-XS time of flight (TOF) mass spec
  • Waters I-Class LC with diode array and QDa mass spec
  • Waters H-Class LC with diode array and QDa mass spec
  • Waters I-Class LC with diode array
  • Waters UPC2 SFC with diode array and chiral columns
  • Waters heartcutting 2D LC-SFC (combination of above two instruments)
  • Advion TLC-MS (x2)

ASF Lab 2

Equipment for purification:

  • Waters Autopurify prep LC with diode array and QDa mass spec

  • Waters 150 AP prep SFC with diode array and QDa mass spec, with chiral and achiral columns 

Key software:

  • Reaction planning: JMP (SAS), Library Studio (Unchained Labs)

  • Data processing: Empower (Waters), MassLynx (Waters), MassWorks (Cerno Bioscience)

  • Data visualization: Spotfire (TIBCO)

ASF Lab 3



External nonprofit

External for-profit












Not available














No charge

Custom quote

Custom quote

Volume discounts are available for internal users

N. Yan, D. Santos-Martins, E. Rennella, B. B. Sanchez, J. S. Chen, L. E. Kay, I. A. Wilson, G. J. Morgan, S. Forli, J. W. Kelly, “Structural basis for the stabilization of amyloidogenic immunoglobin light chains by hydantoins,” Bioorg. Med. Chem. Lett. 2020, 30, article 127356. 

A. X. Jones, L. Wen, L. Legnani, J. Chen, D. G. Blackmond, “Asymmetric amplification in peptide-catalyzed formation of tetrose sugars from nearly racemic amino acids,” J. Systems Chem. accepted.

D. A. Dik, N. Zhang, J. S. Chen, B. Webb, P. G. Schultz, “Semi-synthesis of a bacterium with non-canonical cell wall crosslinks,” J. Am. Chem. Soc. 2020, 142, 10910 – 10913.

C. Zambaldo, E. V. Vinogradova, X. Qi, J. Iaconelli, R. M. Suciu, M. Koh, K. Senkane, S. R. Chadwick, B. B. Sanchez, J. S. Chen, A. K. Chatterjee, P. Liu, P. G. Schultz, B. F. Cravatt, M. J. Bollong, “2-Sulfonyl pyridines as tunable, cysteine-reactive electophiles,” J. Am. Chem. Soc., 2020, 142, 8972 – 8979.

S. Qian, Z.-Q. Li, M. Li, S. R. Wisniewski, J. X. Qiao, J. M. Richter, W. R. Ewing, M. D. Eastgate, J. S. Chen, J.-Q. Yu, “Ligand-enabled Pd(II)-catalyzed C(sp3)–H lactonization using molecular oxygen as oxidant,” Org. Lett. 2020, 22, 3960 – 3963.

J. L. M. Matos, S. A. Green, Y. Chun, V. Q. Dang, R. G. Dushin, P. Richardson, J. S. Chen, D. W. Piotrowski, B. M. Paegel, R. A. Shenvi, “Cycloisomerization of olefins in water,” Angew. Chem. Int. Ed., 2020, 59, ASAP.

D. T. Flood, X. Zhang, X. Fu, Z. Zhao, S. Asai, B. B. Sanchez, E. J. Sturgell, J. C. Vantourout, P. Richardson, M. E. Flanagan, D. W. Piotrowski, D. K. Kölmel, J. Wan, M.-H. Tsai, J. S. Chen, P. Baran, P. E. Dawson, “RASS-enabled S/P–C and S–N bond formation for DEL synthesis,” Angew. Chem. Int. Ed. 2020, 59, 7377 – 7383.

D.-W. Gao, Y. Gao, H. Shao, T.-Z. Qiao, X. Wang, B. B. Sanchez, J. S. Chen, P. Liu, K. M. Engle, “Cascade CuH-catalyzed conversion of alkynes to enantioenriched 1,1-disubstituted products,” Nature Catal. 2020, 3, 23 – 29.

A. M. Romine, K. S. Yang, M. K. Karunananda, J. S. Chen, K. M. Engle, “Synthesis and mechanistic studies of a versatile heteroaryl thioether directing group for Pd(II) catalysis,” ACS Catal. 2019, 9, 7626 – 7640.

A. W. Feldman, V. T. Dien, R. J. Karadeema, E. C. Fischer, Y. You, B. A. Anderson, R. Krishnamurthy, J. S. Chen, L. Li, F. E. Romesberg, “Optimization of replication, transcription, and translation in a semi-synthetic organism,” J. Am. Chem. Soc. 2019, 141, 10644 – 10653.

D. T. Flood, S. Asai, X. Zhang, J. Wang, L. Yoon, Z. C. Adams, B. C. Dillingham, B. B. Sanchez, J. C. Vantourout, M. E. Flanagan, D. W. Piotrowski, P. Richardson, S. A. Green, R. A. Shenvi, J. S. Chen, P. S. Baran, P. E. Dawson, “Expanding reactivity in DNA-encoded library synthesis via reversible binding of DNA to an inert quaternary ammonium support,” J. Am. Chem. Soc. 2019 , 141, 9998 – 10006.

S. Ni, N. M. Padial, C. Kingston, J. C. Vantourout, D. C. Schmitt, J. T. Edwards, M. M. Kruszyk, R. R. Merchant, P. K. Mykhailiuk, B. B. Sanchez, S. Yang, M. A. Perry, G. M. Gallego, J. J. Mousseau, M. R. Collins, R. J. Cherney, P. S. Lebed, J. S. Chen, T. Qin, P. S. Baran, “A radical approach to anionic chemistry: Synthesis of ketones, alcohols, and amines,” J. Am. Chem. Soc. 2019 , 141, 6726 – 6739.

S. K. Nimmagadda, M. Liu, M. K. Karunananda, D.-W. Gao, O. Apolinar, J. S. Chen, P. Liu, K. M. Engle, “Catalytic, enantioselective α-alkylation of azlactones with nonconjugated alkenes by directed nucleopalladation,” Angew. Chem., Int. Ed. 2019, 58, 3923 – 3927.

C. Kingston, M. A. Wallace, A. J. Allentoff, J. N. deGruyter, J. S. Chen, S. X. Gong, S. Bonacorsi, Jr., P. S. Baran, “Direct carbon isotope exchange through decarboxylative carboxylation,” J. Am. Chem. Soc. 2019, 141, 774 – 779.

D. T. Flood, J. C. J. Hintzen, M. J. Bird, P. A. Cistrone, J. S. Chen, P. E. Dawson, “Leveraging the Knorr pyrazole synthesis for the facile generation of thioester surrogates for use in native chemical ligation,” Angew. Chem., Int. Ed. 2018 , 57, 11634 – 11639.

T.-G. Chen, L. M. Barton, Y. Lin, J. Tsien, D. Kossler, I. Bastida, S. Asai, C. Bi, J. S. Chen, M. Shan, H. Fang, F. G. Fang, H.-w. Choi, L. Hawkins, T. Qin, P. S. Baran, “Building C(sp 3)-rich complexity by combining cycloaddition and C–C cross-coupling reactions,” Nature 2018 , 560, 350 – 354.

J. Wang, H. Lundberg, S. Asai, P. Martin-Acosta, J. S. Chen, S. Brown, W. Farrell, R. Dushin, C. J. O’Donnell, A. S. Ratnayake, P. Richardson, Z. Liu, T. Qin, D. G. Blackmond, P. S. Baran, “Kinetically guided radical-based synthesis of C(sp3)–C(sp3) linkages on DNA,” Proc. Natl. Acad. Sci. 2018 , 115, E6404 – E6410 .

D.-W. Gao, Y. Xiao, M. Liu, Z. Liu, M. K. Karunananda, J. S. Chen, K. M. Engle, “Catalytic, enantioselective synthesis of allenyl boronates,” ACS Catal. 2018 , 8, 3650 – 3654.

J. Derosa, V. T. Tran, M. N. Boulous, J. S. Chen, K. M. Engle, “Nickel-catalyzed β,γ-dicarbofunctionalization of alkenyl carbonyl compounds via conjunctive cross-coupling,” J. Am. Chem. Soc. 2017 , 139, 10657 – 10660.