Product Aromatic Aldehyde Final Structure m/z calc RT (min) Purity (%)


.20 (m, 3H), 7.20 -7.12 (m, 2H), 7.07 (d, J = 4.0 Hz, 1H), 7.04 (s, 1H), 6.39 (d, J = 3.9 Hz, 1H), 5.13 (s, 2H), 3.84 (s, 3H), 3.12 (t, 2H), 2.67 (t, 2H), 2.31 (s, 3H). LGW07-20 #52-57 RT: 0.37-0.42 AV: 6 NL: 2.75E3 8.38 (s, 1H), 8.00 -7.89 (m, 3H), 7.56 -7.38 (m, 2H), 7.31 -7.23 (m, 2H), 7.09 (s, 1H), 6.93 (d, J = 3.9 Hz, 1H), 6.30 (d, J = 3.9 Hz, 1H), 3.12 (t, J = 8.8 Hz, 2H), 2.61 (t, J = 8.8 Hz, 2H), 2.31 (s, 3H). 

LCMS

  Conditions: A: H2O-CH2O2: 99.9:0.1, B: ACN-CH2O2: 99.9:0.1; gradient 5% B to 30% B (1 min), gradient 30% B to 95% B (4.5 min), isocratic 95% B (4.5 min), flowrate: 0.4 ml/min. ESI (+) m/z signal found correspond to (M+H) except a: (M-F), b: (M+Na), c: (M+NH4), d: (M-2F+H), e: (M-2Cl+H), and f: (M-Cl); g: Cl replaced by pyrrolidine during synthesis reaction. Purity was determined by integration of all the LCMS absorbance peaks at 254 nm. 


Figure S2 :

 S2 Figure S2: HR ESI negative mode spectrum of compound BAA-37a. HRMS-ESI (m/z): [M-H] - calculated for C26H21BF2N3O2 -: 456.17004; found: 456.16668 (7.4 ppm). 


Figure S3 :

 S3 Figure S3: 1 H NMR spectrum of compound BAA-22a: (400 MHz, DMSO-d6) δ 12.31 (s, 1H), 7.66 (d, J = 16.3 Hz, 1H), 7.63 (s, 1H), 7.56 -7.48 (m, 2H), 7.29 (d, J = 16.3 Hz, 1H), 7.26 -7.20 (m, 3H), 7.20 -7.12 (m, 2H), 7.07 (d, J = 4.0 Hz, 1H), 7.04 (s, 1H), 6.39 (d, J = 3.9 Hz, 1H), 5.13 (s, 2H), 3.84 (s, 3H), 3.12 (t, 2H), 2.67 (t, 2H), 2.31 (s, 3H). 


Figure S4 :

 S4 Figure S4: HR ESI negative mode spectrum of compound BAA-22a. HRMS-ESI (m/z): [M-H] - calculated for C29H25BF3N2O4 -: 533.18650; found: 533.18134 (9.7 ppm). 


Figure S5 :

 S5 Figure S5:1 H NMR spectrum of compound BAA-5a: (400 MHz, DMSO-d6) δ 7.82 (d, J = 16.4 Hz, 1H), 7.68 (d, J = 16.4 Hz, 1H), 7.47 (s, 1H), 6.93 (d, J = 4.0 Hz, 1H), 6.88 (s, 1H), 6.37 -6.16 (m, 4H), 3.96 -3.73 (m, 9H), 3.05 (t, J = 7.7 Hz, 2H), 2.58 (t, J = 7.7 Hz, 2H), 2.25 (s, 3H). 


Figure S6 :

 S6 Figure S6: HR ESI negative mode spectrum of compound BAA-5a. HRMS-ESI (m/z): [M-H] - calculated for C24H24BF2N2O5 -: 469.17518; found: 469.17104 (9.7 ppm). 


Figure S7 :

 S7 Figure S7:1 H NMR spectrum of compound BAA-2a: (400 MHz, DMSO-d6) δ 12.02 (s, 1H), 8.38 (s, 1H), 8.00 -7.89 (m, 3H), 7.56 -7.38 (m, 2H), 7.31 -7.23 (m, 2H), 7.09 (s, 1H), 6.93 (d, J = 3.9 Hz, 1H), 6.30 (d, J = 3.9 Hz, 1H), 3.12 (t, J = 8.8 Hz, 2H), 2.61 (t, J = 8.8 Hz, 2H), 2.31 (s, 3H). 


Figure S8 :

 S8 Figure S8: HR ESI negative mode spectrum of compound BAA-2a. HRMS-ESI (m/z): [M-H] - calculated for C23H19BF2N3O2 -: 418.15439; found: 418.15805 (8.8 ppm). 


Figure S9 :

 S9 Figure S9: 1 H NMR spectrum of compound BAA-39a: (400 MHz, DMSO-d6) δ 8.25 (d, J = 2.5 Hz, 1H), 7.84 (dd, J = 9.0, 2.4 Hz, 1H), 7.62 (d, J = 16.2 Hz, 1H), 7.52 (s, 1H), 7.18 (d, J = 16.2 Hz, 1H), 7.03 (s, 1H), 6.99 (d, J = 3.9 Hz, 1H), 6.58 (d, J = 9.0 Hz, 1H), 6.34 (d, J = 4.0 Hz, 1H), 3.08 (t, J = 11.8 Hz, 2H), 2.55 (t, J = 11.8 Hz, 2H), 2.26 (s, 3H), 2.00 -1.92 (m, 8H). 


Figure S10 :

 S10 Figure S10: HR ESI negative mode spectrum of compound BAA-39a. HRMS-ESI (m/z): [M+H] + calculated for C24H26BF2N4O2 + : 451.21114; found: 451.21296 (4.0 ppm). 


Table S1 :

 S1 Chemical structures and LCMS calculated purity data for BAA library. 


	Product Aromatic Aldehyde Product Aromatic Aldehyde Product Aromatic Aldehyde Product Aromatic Aldehyde Product Aromatic Aldehyde Product Aromatic Aldehyde Product Aromatic Aldehyde Product Aromatic Aldehyde Product Aromatic Aldehyde Product Aromatic Aldehyde Product Aromatic Aldehyde	Final Structure Final Structure Final Structure Final Structure Final Structure Final Structure Final Structure Final Structure Final Structure Final Structure Final Structure	m/z calc m/z calc m/z calc m/z calc m/z calc m/z calc m/z calc m/z calc m/z calc m/z calc m/z calc	m/z exp m/z exp m/z exp m/z exp m/z exp m/z exp m/z exp m/z exp m/z exp m/z exp m/z exp	RT (min) RT (min) RT (min) RT (min) RT (min) RT (min) RT (min) RT (min) RT (min) RT (min) RT (min)	Purity (%) Purity (%) Purity (%) Purity (%) Purity (%) Purity (%) Purity (%) Purity (%) Purity (%) Purity (%) Purity (%)
	Product Aromatic Aldehyde	Final Structure	m/z calc	m/z exp	RT (min)	Purity (%)
	BAA-12a BAA-19a BAA-23b BAA-28b BAA-35b BAA-41b BAA-47a BAA-53a BAA-57b BAA-64a BAA-71a		456.16 462.14 758.21 616.35 702.22 768.32 468.2 440.17 656.29 480.13 541.16	474.19 c 485.13 b 739.13 a 617.37 703.15 769.33 491.20 b 441.17 657.30 481.11 542.17	7.69 8.94 7.93 6.99 8.49 7.61 8.62 7.57 8.01 7.50 9.06	88 96 89 97 86 94 94 >99 >99 91 >99
	BAA-1b		698.15	699.15	7.83	92
	BAA-13a BAA-20a BAA-24b BAA-29b BAA-36b BAA-42a BAA-48a BAA-54a BAA-58a BAA-65a BAA-72a		428.15 442.14 719.98 604.03 742.17 568.09 525.2 432.1 514.19 464.15 493.16	429.15 443.15 700.98 a 605.03 743.18 501.17 e 548.19 b 433.09 515.18 427.14 d 511.17 c	7.28 8.07 7.46 8.14 8.16 6.17 8.24 7.98 8.20 8.82 8.13	90 98 94 86 94 82 >99 89 >99 88 98
	BAA-2a		419.16	400.16 a	7.66	>99
	BAA-14a BAA-21a BAA-25a BAA-30a BAA-37a BAA-43a BAA-49b BAA-55a BAA-59a BAA-66a BAA-73a		442.17 516.2 524.73 491.18 457.18 534.13 638.21 460.19 535.15 497.09 502.09	465.16 b 497.21 a 547.12 b 492.19 438.18 a 501.17 f 619.21 a 461.18 553.16 c 498.10 503.08	9.153 9.13 9.30 7.41 5.75 6.13 6.58 7.30 7.37 9.09 7.95	83 95 93 96 88 94 >99 >99 96 93 >99
	BAA-3a		566.07	567.95	8.07	98
	BAA-15a BAA-21b BAA-25b BAA-31b BAA-37b BAA-44b BAA-50a BAA-55b BAA-60b BAA-67a BAA-74a		450.19 740.29 756.14 536.28 622.24 876.26 460.19 628.26 644.07 517.18 604.22	451.19 741.29 757.15 497.15 d 623.24 877.27 483.18 b 629.26 645.08 518.18 627.21 b	8.83 7.82 7.88 6.34 5.78 8.15 8.07 6.89 8.11 9.02 8.02	96 92 95 94 >99 92 >99 89 99 92 92
	BAA-3b		840.02	863.25 b	8.21	97
	BAA-16a BAA-22a BAA-26b BAA-32a BAA-38a BAA-45a BAA-50b BAA-56a BAA-61a BAA-68a BAA-74b		422.2 534.19 672.32 517.16 450.2 538.75 628.26 463.13 496.22 463.13 916.32	445.19 b 515.20 a 673.33 478.15 d 451.21 562.14 b 629.25 464.13 497.21 464.14 897.32 a	9.08 8.65 7.56 8.77 6.28 9.29 6.94 5.87 7.32 8.27 7.01	98 94 98 >99 99 >99 >99 >99 98 >99 94
	BAA-4a		478.24	479.24	6.02	>99
	BAA-17a BAA-22b BAA-27b BAA-33a BAA-39a g BAA-45b BAA-51a BAA-56b BAA-62a BAA-69a BAA-75a		456.18 776.27 720.16 536.04 415.11 784.17 491.18 634.15 431.16 525.1 501.21	479.17 b 777.28 683.22 d 559.02 b 451.21 g 785.17 514.16 b 635.15 449.16 c 526.09 482.22 a	9.09 7.51 7.19 7.94 5.99 8.24 7.59 7.84 6.81 9.08 10.99	85 90 97 98 94 96 89 84 >99 >99 >99
	BAA-5a		470.18	471.19	8.26	>99
	BAA-18a BAA-23a BAA-28a BAA-34b BAA-40b BAA-46b BAA-52a BAA-57a BAA-63a BAA-70a BAA-75b		486.19 525.16 454.24 702.07 876.26 740.29 498.13 474.2 479.14 525.16 710.31	509.18 b 526.18 435.28 a 683.06 a 877.27 741.28 499.12 475.21 502.15 b 526.18 711.32	8.94 9.05 6.69 7.69 7.96 7.69 7.86 6.10 7.05 8.95 6.38	92 >99 88 94 89 94 83 85 93 99 94

Table S2 :

 S2 Spectroscopic and photochemical properties of BAA library. 


	Product Product	λmax ABS (nm) λmax ABS (nm)	λmax EM (nm) λmax EM (nm)	Stokes Shift (nm) Stokes Shift (nm)	Φ fl Φ fl	FWHM FWHM
	Product BAA-31b BAA-64a	λmax ABS (nm) 576 576	λmax EM (nm) 588 593	Stokes Shift (nm) 12 17	Φ fl 0.28 0.80	FWHM 34 37
	BAA-32a BAA-65a	574 606	584 622	10 16	0.23 0.21	32 54
	BAA-1b BAA-33a BAA-66a	580 575 587	597 587 598	17 12 11	0.62 0.15 0.28	40 35 34
	BAA-2a BAA-34b BAA-67a	601 570 587	635 581 598	34 11 11	0.62 0.96 0.15	57 31 61
	BAA-3a BAA-35b BAA-68a	569 571 585	579 580 595	10 9 10	0.61 0.25 0.17	31 32 30
	BAA-3b BAA-36b BAA-69a	574 579 577	587 592 589	13 13 12	0.70 0.35 0.85	34 37 30
	BAA-4a BAA-37a BAA-70a	581 568 580	600 578 588	19 10 8	0.43 0.54 0.17	56 55 33
	BAA-5a BAA-37b BAA-71a	592 569 580	615 578 589	23 9 9	0.83 0.55 0.19	47 30 32
	BAA-6a BAA-38a BAA-72a	609 579 580	643 581 590	34 2 10	0.18 0.07 0.40	64 33 31
	BAA-7a BAA-39a BAA-73a	582 606 579	600 657 593	18 51 14	0.29 0.19 0.55	63 79 46
	BAA-7b BAA-40b BAA-74a	581 583 584	600 601 602	19 18 18	0.43 0.26 0.15	56 45 59
	BAA-8a BAA-41b BAA-74b	594 582 583	623 602 600	29 20 17	0.50 0.36 0.22	61 47 51
	BAA-9a BAA-42a BAA-75a	569 570 614	579 580 663	10 10 49	0.35 0.36 0.08	32 30 91
	BAA-10b BAA-43a BAA-75b	632 569 605	714 579 660	82 10 55	0.01 0.45 0.18	102 31 91
	BAA-11a BAA-44b BAA-76a	575 582 613	589 600 634	14 18 21	0.86 0.28 0.21	33 43 55
	BAA-12a BAA-45b BAA-77a	589 570 603	616 579 634	27 9 31	0.10 0.50 0.50	88 30 61
	BAA-13a BAA-45a BAA-78a	576 571 581	586 580 592	10 9 11	0.19 0.22 0.19	44 31 46
	BAA-14a BAA-46b BAA-78b	594 572 579	607 585 593	13 13 14	0.44 0.61 0.37	70 33 39
	BAA-15a BAA-47a BAA-79a	581 589 606	597 611 630	16 22 24	0.42 0.33 0.63	39 47 49
	BAA-16a BAA-48a	552 603	610 641	58 38	0.22 0.45	78 60
	BAA-17a BAA-49b	579 571	591 580	12 9	0.59 0.14	42 33
	BAA-18a BAA-50a	577 571	593 581	16 10	0.65 0.28	37 33
	BAA-19a BAA-50b	582 572	595 581	13 9	0.64 0.12	35 34
	BAA-20a BAA-51a	577 594	585 607	8 13	0.15 0.06	31 42
	BAA-21a BAA-52a	585 577	611 585	26 8	0.51 0.04	46 51
	BAA-21b BAA-53a	588 570	608 581	20 11	0.54 0.44	50 30
	BAA-22a BAA-54a	585 573	602 581	17 8	0.39 0.04	49 46
	BAA-22b BAA-55a	582 576	601 592	19 16	0.27 0.75	46 35
	BAA-23a BAA-55b	592 575	603 591	11 16	0.23 0.75	30 38
	BAA-23b BAA-56a	580 585	588 595	8 10	0.19 0.91	32 32
	BAA-24b BAA-56b	570 586	579 597	9 11	0.29 0.15	32 35
	BAA-25a BAA-57a	571 574	580 590	9 16	0.19 0.75	32 45
	BAA-25b BAA-57b	572 575	580 591	8 16	0.18 0.75	32 38
	BAA-26b BAA-58a	582 572	604 582	22 10	0.30 0.70	51 30
	BAA-27b BAA-59a	575 571	588 581	13 10	0.33 0.53	35 30
	BAA-28a BAA-60b	480 588	592 604	112 16	0.04 0.47	52 37
	BAA-28b BAA-61a	580 573	598 587	18 14	0.58 >0.99	43 35
	BAA-29b BAA-62a	569 579	580 594	11 15	0.13 0.68	37 33
	BAA-30a BAA-63a	607 592	643 607	36 15	0.43 0.43	58 39

Table S3 :

 S3 Organelle specificity of BAA Library in fixed U2OS cells. 


	Images are 168x135 µm and shown with contrast optimized for each dye to show cellular structure
	localization.

Table S4 :

 S4 Molecular properties, organelle specificity, and SBR for the BAA library. 


	0 Hz,
	1H), 7.05 (s, 1H), 6.46 (d, J = 4.0 Hz, 2H), 3.11 (t, J = 7.8 Hz, 2H), 2.53 (t, J = 7.8 Hz, 2H), 2.33
	(s, 3H).

Figure S1:1 H NMR spectrum of compound BAA-37a: (400 MHz, DMSO-d6) δ 8.94 (dd, J = 2.5, 0.9 Hz, 1H), 8.62 (dd, J = 4.8, 1.6 Hz, 1H), 8.13 (ddd, J = 8.0, 2.5, 1.6 Hz, 1H), 7.88 (t, J = 1.7 Hz, 1H), 7.80 -7.69 (m, 4H), 7.60 (t, J = 7.7 Hz, 1H), 7.56 -7.49 (m, 2H), 7.15 (d, J = 4. 
Supplementary Information

Varied Length Stokes Shift BODIPY-Based Fluorophores for Multicolor Microscopy BAA compounds showed localization to cytosol (c), vesicles (v), and nucleolar (n) regions.
Product Aromatic Aldehyde Final Structure m/z calc RT (min) Purity (%)