synergistic combination of case algorithms and dft chemical … · case-dft structure elucidation...

SYNERGISTIC COMBINATION OF CASE ALGORITHMS AND DFT CHEMICAL SHIFT PREDICTIONS FOR STRUCTURE ELUCIDATION, VERIFICATION AND REVISION

Alexei V. Buevich (Merck and Co.) Mikhail E. Elyashberg (ACD/Labs)

ACD/Labs NJ Software Symposium

February 7, 2018 Princeton NJ

2

Molecular Structure Analysis

2

Experimental data

Molecular Model

Structure Elucidation Structure Reconstruction

De Novo Structure Analysis

Structure Verification

Computer-Assisted Structure Elucidation

3

Pioneers of Computer-Assisted Structure Elucidations

3

J. Lederberg E. Feigenbaum C. Djerassi

Stanford, USA J. Am. Chem. Soc., 1969, V. 91, p. 2973

M. Munk S-I. Sasaki

Arizona, USA J. Org. Chem., 1969, V. 34, p. 3800

Sendai, Japan Anal. Chem., 1968, V. 40, p. 2220

Moscow, USSR J. Appl. Spectrosc., 1968, v.8, p.696

M.E. Elyashberg L.A. Gribov

4

CASE expert systems based on MS and 2D NMR data

LSD (J.-M. Nuzillard, France) SESAMI (M.E. Munk, USA) CISOC-SES (C. Peng, USA-China) LUCY (C. Steinbeck, Germany) COCON (T. Lindel, Germany) SENECA (C. Steinbeck, Germany) CMC-se (Bruker) Mnova Structure Elucidator (Mestrelab Research) ACD/Structure Elucidator (ACD/Labs)

5

Workflow of ACD/Structure Elucidator algorithm 1) Molecular formula from MS

2) NMR data: 1H, 13C, COSY, HSQC, HMBC

3) Molecular connectivity diagram (MCD)

4) Generation (Strict or Fuzzy) of all possible

constitutional isomers from MCD

5) Empirical chemical shift predictions Fragmental approach (HOSE code based) Method of increments (additive rules) Artificial neural networks (ANN)

6) Ranking structures based on chemical shift deviations:

standard deviation, average deviation, max deviation

M. Elyashberg, A. Williams Computer-based Structure Elucidation from Spectral Data. The Art of Solving Problems. Springer, Heidelberg, 2015, 454 p.

MCD

6

Two types of situations when CASE programs have failed to distinguish the correct structure based on COSY, HSQC and HMBC data

a) the correct structure is on the first position, but its’ average

deviations of chemical shifts are too large (5-6 ppm)

b) the correct structure is either first or among several top-ranked structures with acceptable but very similar deviations

How can CASE algorithms be improved?

7

Incorporate more experimental data:

1,1-ADEQUATE and 1,n-ADEQUATE LR-HSQMBC RDC/RCSA

Improve accuracy of proton/carbon chemical shift predictions

QM

M. Elyashberg, K. Blinov, Y. Smurnyy et al. Magn. Reson. Chem. 2010, 48, 219-229

DFT calculations of NMR chemical shifts

• Recommendations by Rablen, Bally and Tantillo: (http://cheshirenmr.info)

• More than 250 different combinations of functionals and basis sets for nearly all possible situations (limited to organic molecules and natural products)

Scaling factors for calculating chemical shifts (δ) from isotropic shieldings (σ): Scaling factors deemed to take into account the effect of vibrational corrections on chemical shifts (E. E. Kwan and R. Y. Liu JCTC 2015, 11, 5083)

9

CASE-DFT structure elucidation

1) CASE analysis based on MS and NMR data

2) Structures are ranked based on HOSE (NN) predicted carbon chemical shifts

3) Up to Six top-ranked structures by CASE are analyzed by DFT: a) Conformational analysis by MM b) Geometry optimization of the lowest energy conformations by DFT c) Chemical shift calculation by DFT for the lowest energy conformations d) Boltzmann averaging of chemical shifts

4) Structures are ranked based on chemical shifts calculated using DFT

5) The correct structure is selected based on the lowest RMSD (MAE, SD, max_δ or DP4+)

1. Aquatolide (unusual scaffold)

10

OO

O

O

O

O

• Sesquiterpenoid lactone isolated from Asteriscus aquaticus

• Revision was done based on extensive NMR analysis of coupling constants, NOEs, and chemical shifts + DFT analysis of 60 structures + X-ray

1. A. San Feliciano, M. Medarde, J. M. Miguel del Corral, A. Aramburu, M. Gordaliza, A. F. Barrero, Tetrahedron Lett. 1989, 30, 2851. 2. M.W. Lodewyk, C. Soldi, P.B. Jones, M. M. Olmstead, J. Rita, J. T. Shaw, D. J. Tantillo, J. Am. Chem. Soc. 2012, 134,18550.

Original[1] Revised[2]

1989 2012 Asteriscus aquaticus

CASE study of Aquatolide

11

Carbon δCexp δCcalc CHn δHexp JHH, Hz HMBC (H to C) C 1 84.2 87.69 CH 4.48 t(2.2) C 12, C 15, C 3, C 10, C 14 C 2 54.54 49.01 CH 3.26 dd(7.3, 2.5) C 11, C 8, C 3, C 10 C 3 62.83 54.68 C C 4 22.15 31.27 CH2 1.96 m

C 4 22.15 31.27 CH2 2.52 m C 2, C 6, C 10, C 12, C 3, C

5 C 5 28.63 23.36 CH2 2.35 m C 5 28.63 23.36 CH2 2.03 m C 6 131.1 143.34 CH 5.85 ddt(4.7,3.1,1.5) C 4, C 13, C 8 C 7 135.08 136.93 C C 8 211.94 199.27 C

C 9 54.45 51.52 CH 2.92 s C 8, C 7, C 1, C 10, C 2, C

3, C 11

C 10 62.59 49.53 CH 2.64 dd(7.3,1.8) C 11, C 1, C 15, C 8, C 2, C

9, C 14, C 4 C 11 41.86 40.09 C C 12 177.5 176.04 C C 13 22.22 19.56 CH3 1.87 q(2.0) C 7, C 8, C 6 C 14 22.62 12.31 CH3 1.05 s C 15, C 1, C 11, C 10 C 15 22.84 22.77 CH3 1.19 s C 11, C 14

MCD

1H, 13C, COSY, HSQC, HMBC

CASE study of Aquatolide

12

• Only three structures were generated by ACD/Structure Elucidator (tg=0.05s)

• No original structure in the output file (!)

• The revised structure is ranked first, but all three structures have large chemical shift deviations

revised

CASE-DFT study of Aquatolide

13

The lowest RMSD and max_δ are predicted for the revised structure (!)

CH3

H3CCH3

O

O

O

6

10

4

5

78 H3C

CH3

CH3

O

O

O12

23

1

119

15

14

13

6

104

5

7

8

12

2

3

1

11

9

15

14

13

H3C CH3

O

O

O

6

10

45

7

8

12

2

3

1

119

1514

13

Structure #1 (2) Structure #2 Structure #3

Experimental Structure #1 Structure #2 Structure #3 Carbons δCexp δCcalc δCcalc δCcalc

C 1 84.2 83.28 87.38 85.33 C 2 54.54 54.53 69.43 53.46 C 3 62.83 63.17 54.56 45.07 C 4 22.15 22.80 36.46 22.29 C 5 28.63 30.69 33.12 32.50 C 6 131.1 135.07 160.44 146.18 C 7 135.08 137.29 132.61 138.82 C 8 211.94 211.99 197.42 201.88 C 9 54.45 54.97 55.04 49.13

C 10 62.59 64.91 79.42 50.35 C 11 41.86 44.91 48.70 48.82 C 12 177.5 177.40 172.69 176.12 C 13 22.22 22.94 13.69 16.92 C 14 22.62 20.63 19.75 18.37 C 15 22.84 20.89 25.47 27.87

RMSD, ppm 1.82 11.38 7.65 max_δ, ppm 3.97 29.34 17.76

Gaussian09: mPW1PW91-PCM/6-311+G(2d,p)//B3LYP/6-31+G(d,p) A.V. Buevich, M. E. Elyashberg, J. Nat. Prod. 2016, 79, 3105.

Lessons of Aquatolide story

14

CASE analysis would have prevented the publication of erroneous structure CASE analysis significantly reduces the number of potential structures that needs to be verified by DFT calculations

CH3

H3CCH3

O

O

O

6

10

4

5

78 H3C

CH3

CH3

O

O

O12

23

1

119

15

14

13

6

104

5

7

8

12

2

3

1

11

9

15

14

13

H3C CH3

O

O

O

6

10

45

7

8

12

2

3

1

119

1514

13

Structure #1 (2) Structure #2 Structure #3

M.W. Lodewyk, C. Soldi, P.B. Jones, M. M. Olmstead, J. Rita, J. T. Shaw, D. J. Tantillo, J. Am. Chem. Soc. 2012, 134,18550.

A.V. Buevich, M. E. Elyashberg, J. Nat. Prod. 2016, 79, 3105.

Structure determined based

on CASE-DFT

2. Coniothyrione (proton-deficient)

15

• The original structure of coniothyrione (isolated from an extract derived from a strain of Coniothyrium cerealis MF7209) was proposed based on the absence of HMBC cross-peak between olefinic proton H4 and carbonyl carbon C1 (!).

• The structure of coniothyrione was revised based on 1,1-ADEQUATE experiments and DFT analysis of JCC, JHC couplings, and carbon chemical shifts.

3. Ondeyka, J. G.; Zink, D.; Basilio, A.; Vicente, F.; Bills, G.; Diez, M. T.; Motyl, M.; Dezeny, G.; Byrne, K.; Singh, S. B. J. Nat. Prod. 2007, 70, 668. 4. Kong, F.; Zhu, T.; Pan, W.; Tsao, R.; Pagano, T. G.; Nguyen, B.; Marquez, B. Magn. Reson. Chem. 2012, 50, 829. 5. Martin, G. E.; Buevich, A. V.; Reibarkh, M.; Singh, S. B.; Ondeyka, J. G.; Williamson, R. T. Magn. Reson. Chem. 2013, 51, 383.

Original[3] Revised[4,5]

2007 2012, 2013

O

OH O HO

Cl

O

O12

4

13

8O

OH O HO

Cl

O

O

CASE study of Coniothyrione

16

Carbon δC δC calc XHn δH JHH, Hz HMBC (H to C) C1 168.7 172.74 C C2 79.8 78.01 C C3 127.2 132.49 C C4 143.1 129.25 CH 7.2 s C2, C5, C14 C5 164.5 154.7 C C7 155.7 156.53 C C8 108.1 108.9 CH 7.22 d(8.5, 1.0) C10, C12 C9 135.8 137.35 CH 7.7 t(8.5) C7, C11

C10 112.7 112.14 CH 6.9 dd(8.5, 1.0) C8, C12 C11 160.6 160.56 C C12 110.7 109.78 C C13 176 175.24 C C14 120.8 114.22 C C15 52.9 51.97 CH3 3.64 s C1 O1 OH 12.4 s C10, C11, C12

CH352.90(ob)

C79.80(ob) CH

108.10

C110.70

CH112.70

C120.80

C127.20

CH135.80

CH143.10

C155.70

C160.60(ob)

C164.50(ob) C

168.70(ob)

C176.00(ob)

O

O

O

O

OOH

Cl

H

MCD

Coniothyrione is a proton-deficient molecule C14H9ClO6 No ADEQUATE data were used in CASE study (!)

CASE study of Coniothyrione

17

CH3

OH

O

O

O

O

OH

Cl

dA(13C): 3.137dN(13C): 3.480dI(13C): 5.351max_dA(13C): 15.130

#1 CH3

OH

O

O

O

O

OH

Cl

dA(13C): 3.410 dN(13C): 3.072dI(13C): 3.398max_dA(13C): 13.850

#2 CH3

OH

O

O

O

O

OH

Cl


#3

CH3

OH

OO

O

O

OHCl


#4

CH3

OH

O

O

O OOH

Cl


#5

CH3

OH

OO

O

OOH Cl


#6

Revised

157803 structures were generated by ACD/Structure Elucidator, only 14976 passed spectral and structural filtering (tg=1 min) The revised structure was ranked second (!), the original structure was ranked 18th


CASE-DFT study of Coniothyrione

18

Exper. Structure

#1

Structure #2

(revised) Structure

#3 Structure

#4 Structure

#5 Structure

#6 Labels δC δCcalc δCcalc δCcalc δCcalc δCcalc δCcalc

1 168.7 171.3 172.0 165.9 165.6 164.0 160.4 2 79.8 81.6 79.6 69.6 85.1 84.4 102.9 3 127.2 142.7 135.6 146.1 147.1 140.9 156.3 4 143.1 125.4 144.9 134.1 135.8 136.1 125.7 5 164.5 171.0 163.8 160.8 155.7 163.8 164.1 7 155.7 154.6 154.7 158.8 160.3 159.6 154.7 8 108.1 105.3 105.5 105.3 101.5 103.8 105.7 9 135.8 134.8 134.3 125.3 126.4 126.7 134.1

10 112.7 111.9 112.0 106.5 108.9 109.1 111.8 11 160.6 160.5 160.5 145.3 150.2 148.9 160.8 12 110.7 109.8 110.3 110.2 108.8 108.6 110.1 13 176.0 173.9 172.9 159.1 173.1 180.5 172.3 14 120.8 117.2 120.6 121.1 124.7 122.7 117.3 15 52.9 54.1 53.7 53.8 53.2 51.7 52.0

RMSD - 6.75 2.76 9.46 7.86 6.40 11.29 max_δ - 17.71 8.39 18.94 19.87 13.67 29.07

Only top 6 structures had to be analyzed by DFT (!) The lowest RMSD and max_δ are predicted for the revised structure #2 (!) (Structure #1 was also rejected based on JCH-coupling analysis)

Gaussian09: mPW1PW91-PCM/6-311+G(2d,p)//B3LYP/6-31+G(d,p)

O

OH O HO

Cl

O

O12

413

89

1011 12

7

14

5 3

#1 #2

15

OHO

Cl

O

O

OOH

12

413

8

9

1011 12

7

14

5

3

15

OH

1

2

4

13

8

9

1011 12

7

14

5

3

15

O

O OH

Cl

O O

OH

1

2

4

138

9

1011 12

7

14

5

3

15

O

O O

OH

O Cl

OH 1

2

4

138

9

1011 12

7

14

5

3

15

OOH

O Cl

O

OO

OH O HO

1

2

413

89

1011 12

7

14

5 3

15

Cl

OO

#3 #4

#5 #6


3. Oroidin (heavy atoms)

19

• Oroidin (C11H10Br2N4O), a highly proton-deficient bromopyrrole (5), was isolated from the sponge Agelas oroides

• Oroidin has been extensively studied by IR, NMR, X-ray crystallography and was confirmed by direct synthesis

• The structure of oroidin was conclusively identified by the decidedly lowest average deviations by COCON program6

6. M. Köck, J. Junker, T. Lindel, Org. Lett. 1999, 1, 2041-2044. 7. T. Lindel, J. Junker, M. Köck, Eur. J. Org. Chem. 1999, 573-577 8. S. Rasapalli, V. Kumbam, A. N. Dhawane, J. A. Golen, C. J. Lovely, A. L. Rheingold, Org. Biomol. Chem. 2013, 11, 4133-4137.

NH

O

Br

Br HN N

NHNH2

3

2

4

5

Agelas oroides 5

CASE study of Oroidin

20

156 structures were predicted by ACD/Structure Elucidator

Correct structure of oroidin was ranked first, though structure #3 had very similar average deviations and max_δ, thus prompting DFT analysis

NH

O

Br

Br HN N

NHNH2

3

2

4

5

NH2

NH

NH

NHN

O

BrBr

NH2

NH

NH

NHN

O

BrBr4

5

NH2

NH

NH

NHN

O

Br

Br

NH2

NH

NH

NHN

O

Br

Br

5

correct

CASE-DFT study of Oroidin

21

Three top-ranked structures were calculated using SPARTAN program (H, C, N, O, S, Si, P, F, Cl, Br) The lowest RMSD and max_δ are predicted for the correct structure 5 SPARTAN: EDF2/6-31G(d)//B3LYP/6-31+G(d,p)

Carbons Exp. 6 (5) 7 (5-3) 8 (5-4) 2 128.0 127.7 128.8 126.7 3 113.0 111.4 117.2 121.0 4 98.0 100.1 97.8 100.2 5 105.0 102.6 97.9 103.4 6 159.0 161.4 161.5 161.2

RMSD, ppm - 1.93 3.87 3.95 max_δ, ppm - 2.4 7.1 8.0

HNBr

O

HN

Br 32

4

5 6

HNBr

BrO

HN

3 24

5 6

HN

BrO

HN

Br

3

2

45

6

A.V. Buevich, M. E. Elyashberg, Magn. Reson. Chem. 2017, DOI: 10.1002/mrc.4645

4. Epoxyroussoenone (proton-deficient and chiral)

22

• Epoxyroussoenone (11) was isolated from a culture broth of Roussoella japanensis KT1651.

• Structure was determined using 1D and 2D NMR spectroscopy supported by DFT calculations of 13C chemical shifts and ECD spectra. Configuration was determined based on NOE and ECD data.

• Only two alternative structures, 11 and 12, have been examined, which appears to be insufficient considering its proton-deficient nature (C15H14O7).

Honmura, Y.; Takekawa, H.; Tanaka, K.; Maeda, H.; Nehira, T.; Hehre, W.; Hashimoto, M. J. Nat. Prod. 2015, 78, 1505-1510

1

4

9

76

3

O

OH

O

OH

OH

O

O

OHOOH

OO

HO

O

10

5

11 12

CASE study of Epoxyroussoenone

23

CH321.05(fb)

CH355.41(ob) C

61.81(ob)

CH65.09(ob) CH

68.45(ob)

C88.25(ob)

CH103.31(fb)

CH104.53(fb) CH

104.70(fb)

C108.51(fb)

C134.58(fb) C

158.39(ob)

C161.30(ob)

C170.26(ob)

C189.12(ob)

OO

OO

OHOH

OH

MCD

CH3

CH3

OH OH

OH

O

O

O

O


#1

CH3CH3

OH OH

OH

O

O

O

O


#2

CH3

CH3

OH

OHOHO

O

O

O


#3

CH3

CH3

OH OHOH

O

O

O

O


#4

CH3

CH3

OH OHOH

OO

O

O


#5

CH3CH3

OH

OHOHO

O

O

O


#6

1500 structures were generated by ACD/Structure Elucidator, only 13 passed spectral and structural filtering (tg=1 s). The correct structure was ranked second (!). The alternative structure 11 was rejected (124th position). Instead, 6 plausible structures would need to be examined.

correct


CASE-DFT study of Epoxyroussoenone

24

4 diastereomers (A, B, C, D) for each of the top-ranked six structures were analyzed by DFT Structures #1 and #2 may have two conformations. Only chemical shifts of the lowest energy conformations were used. Correct isomer is #2A

O

OH

O

OH

OH

O

OO

OH

O

OH

OH

O

OO

OH

O

OH

OH

O

OO

OH

O

OH

OH

O

O

O

OH

OH

O

O

OH

O

O

OH

OH

O

O

OH

O

O

OH

OH

O

O

OH

O

O

OH

OH

O

O

OH

O

OH

OH

OOH

O

O

O

OH

OH

OOH

O

O

O

OH

OH

OOH

O

O

O

OH

OH

OOH

O

O

O

OHOH

O

O

O

OH

O

OHOH

O

O

O

OH

O

OHOH

O

O

O

OH

O

OHOH

O

O

O

OH

O

OOH

O

OH

O

O

OOH

O

OH

O

O

OOH

O

OH

O

O

OOH

O

OH

O

O

OH OH OH OH

OOH

O

O

OHO

OH

OOH

O

O

OHO

OH

OOH

O

O

OHO

OH

OOH

O

O

OHO

OH

#1A #1B #1C #1D

#2A #2B #2C #2D

#3A #3B #3C #3D

#4A #4B #4C #4D

#5A #5B #5C #5D

#6A #6B #6C #6D


CASE-DFT(13C) study of Epoxyroussoenone

25

RMSD and max_δ between experimental and DFT-calculated δ(13C) for six top-candidate structures of epoxyroussoenone and their stereoisomers A, B, C and D The lowest RMSD and max_δ were found for the first two top-ranked structures. The correct #2A structure has similar RMSD with #2B and #1B.

0.00

2.00

4.00

6.00

8.00

10.00

12.00

14.00

16.00

1A 1B 1C 1D 2A 2B 2C 2D 3A 3B 3C 3D 4A 4B 4C 4D 5A 5B 5C 5D 6A 6B 6C 6D

RMSD

and

max

_δ, p

pm

Structures

RMSD

max_δ

Gaussian09: mPW1PW91-PCM/6-311+G(2d,p)//B3LYP/6-31+G(d,p) A.V. Buevich, M. E. Elyashberg, J. Nat. Prod. 2016, 79, 3105.

CASE-DFT(13C) study of Epoxyroussoenone

26

RMSD(C5,C10) and ∆∆δ(C5,C10) for the most critical C5 and C10 carbon chemical shifts were calculated. The lowest RMSD(C5,C10) and ∆∆δ(C5,C10) were found for the correct structure and correct isomer #2A (11).

Gaussian09: mPW1PW91-PCM/6-311+G(2d,p)//B3LYP/6-31+G(d,p)

0

5

10

15

20

25

1A 1B 1C 1D 2A 2B 2C 2D 3A 3B 3C 3D 4A 4B 4C 4D 5A 5B 5C 5D 6A 6B 6C 6DRM

SD(C

5,C1

0) a

nd ∆

∆δ(

C5,C

10),

ppm

Structures

RMSD(C5,C10)

∆∆δ(C5,C10)O

OH

O

OH

OH

O

O10

5

O

OH

OH

O

O

10

5OH

O

#1 #2

∆∆δ(C5,C10) = |(∆δ(C5,C10)exp - ∆δ(C5,C10)calc|


CASE-DFT(1H) study of Epoxyroussoenone

27

RMSD(OH) and max_δ(OH) for 1H chemical shifts of the three OH groups in four diastereomers of the six top-ranked structures of epoxyroussoenone The lowest RMSD(OH) and max_δ(OH) were found for the correct structure and correct isomer #2A (11).

0

1

2

3

4

5

6

7

8

1A 1B 1C 1D 2A 2B 2C 2D 3A 3B 3C 3D 4A 4B 4C 4D 5A 5B 5C 5D 6A 6B 6C 6D

RMSD

(OH)

and

max

_δ, p

pm

Structures

RMSD(OH)

max_δ

OH

OH

OOH

O

O

O

OHOH

O

O

O

OH

O

OOH

O

OH

O

O

OH OOH

O

O

OHO

OH

O

OH

O

OH

OH

O

OO

OH

OH

O

O

OH

O

#1 #2

#5 #6

#3 #4

(M. G. Chini, R. Riccio, G. Bifulco Eur. J. Org. Chem. 2015, 1320)


Conclusions

28

Synergistic combination of CASE and DFT:

Addition of the DFT to CASE expert systems broadens the range of amenable to CASE structural problems: - molecules with unusual scaffolds - configurational isomers - conformationally flexible molecules (A.V. Buevich & M.E. Elyashberg MRC 2017, DOI: 10.1002/mrc.4645) DFT-based analysis of molecular structures as a method of structure verification in combination with CASE becomes a true structure elucidation method

Acknowledgments

29

Gary Martin (Merck) Thomas Williamson (Merck) Ryan Cohen (Merck) Dimitris Argyropoulos (ACD/Labs) Dean Tantillo (UCD) Masaru Hashimoto (Hirosaki University)

THANK YOU

synergistic combination of case algorithms and dft chemical … · case-dft structure elucidation...

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