Applying Computer Assisted Structure Elucidation Algorithms For The Purpose Of Structure Validation – Revisiting The NMR Assignments Of Hexacyclinol

Applying Computer Assisted Structure Elucidation Algorithms For The Purpose Of

Structure Validation – Revisiting The NMR Assignments Of Hexacyclinol

A.J. Williams*
Advanced Chemistry Development, Inc., 110 Yonge Street,
14th floor, Toronto, Ontario, Canada, M5C 1T4

M.E. Elyashberg
Advanced Chemistry Development, Moscow Department, 6
Akademik Bakulev Street, Moscow 117513, Russian Federation

D.C. Lankin
Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy,
University of Illinois at Chicago, Chicago, Illinois 60612-7231

G.E. Martin
Schering-Plough Research Institute, Rapid Structure
Characterization Laboratory, Pharmaceutical Sciences, Summit, NJ 07901

W.F. Reynolds
Dept of Chemistry, University of Toronto, 80 St George St., Toronto, Ontario M5S 3H6, Canada

and

J.A. Porco Jr., and C.A. Singleton●
Dept. of Chemistry and Center for Chemical Methodology and Library Development,
Boston University, 24 Cummington Street, Boston, MA 02215

●
Now working at : Waters Corporation, 34 Maple Street, Milford, MA, 01757,

* To whom inquiries should be addressed

antony.williams@chemspider.com
904 Tamaras Circle
Wake Forest
NC-27597

1

Abstract
Computer-Assisted Structure Elucidation (CASE) using a combination of 1D and 2D

NMR data has been available for a number of years. These algorithms can be considered as

“logic machines” capable of deriving all plausible structures from a set of structural constraints

or “axioms”, defined by the spectral data and associated chemical information or prior

knowledge. CASE programs allow the spectroscopist not only to determine structures from the

spectral data but also to study the dependence of the proposed structure on changes to the set of

axioms. In this article we describe the application of the ACD/Structure Elucidator expert system

to resolve the conflict between two different hypothetical hexacyclinol structures derived by

different researchers from the NMR spectra of this complex natural product. It has been shown

that the combination of algorithms for both structure elucidation and structure validation

delivered by the expert system enables the identification of the most probable structure as well as

the associated chemical shift assignments.

2

1. Introduction

In recent years Computer Assisted Structure Elucidation (CASE) has offered an additional

option to scientists challenged by difficult chemical structure elucidation problems. The reasons

for considering CASE methods should be obvious – there may be significant time-savings when

applying algorithmic approaches; the subjective bias of a scientist can be reduced relative to an

algorithm; for the thought process associated with the analysis of a large and diverse data

collection made up of spectrum-structural information used to elucidate chemical structure offers

a significant logical and combinatorial challenge. The nature of this process was already revealed

in the pioneering works published in the late 60s and 70s.1-4 When scientists attempt to solve

structural problems they logically draw definitive structural conclusions from a set of spectral

data and a priori knowledge assembled into a set of initial axioms. It has been shown5 that the

definition of a spectrum-structural problem is equivalent to formulating a specific axiomatic

theory.

The solution of a structural problem using 2D NMR spectroscopy data can be divided into

four main stages:

1. Prepare the experimental data to create spectrum-structure axioms that serve as the basis

of the structure elucidation process. This stage encompasses both raw data processing and

peak picking. 1D and 2D peak tables are produced as an output from this stage.

2. Creating axioms and hypotheses on the basis of NMR peak tables. The information

contained in the peak tables is considered as true and consistent. The following axioms

are the most common: a) If the hydrogen atom H(i) shows a HSQC (HMQC) correlation

with the carbon atom C(j), then the atom H(i) is attached to the atom C(j); b) If the

hydrogen atom H(i) attached to the carbon atom C(i) shows a COSY correlation with the

hydrogen atom H(j) attached to the carbon atom C(j), then carbons C(i) and C(j) make up

a chemical bond in a molecule; c) If the hydrogen atom H(i) shows a HMBC correlation

to a carbon atom C(j), then the distance between those atoms in a molecule is 2 or 3

3

bonds; d) If the hydrogen atom H(i) shows a NOESY (ROESY) correlation with the

hydrogen atom H(j), then the distance through space between atoms H(i) and H(j) is less

than 5 Å. Additional structural constraints are produced on the basis of chemical

knowledge including information regarding sample origin and associated structural

knowledge as well as Bredt’s rule, etc.)

3. The logical inference of all direct structural conclusions, if one is possible, comes from

following the set of axioms outlined above. These conclusions form a chemical structure

file where each structure within the file has to satisfy all the axioms applied (i.e. be

entirely consistent with the experimental data) and has to contain the assigned

experimental chemical shifts.

4. The verification of all structural hypotheses proceeds in order to choose the most

probable solutions consistent with the data. For this purpose the prediction of NMR

spectra associated with the candidate structures in combination with specific chemical

considerations is applied and hypothetical structures are rank ordered based on the

agreement between the experimental data and the algorithmically generated structures.

If all initial axioms used to deduce the structural formula of an unknown contain no

contradictions then the structural file produced will be valid6 and will contain the actual

structure. It is evident that if at least one of the axioms in the set is false or contradicts and of the

other axiom(s) then the correct structure will not be determined. A contradictory system of

axioms simply produces no structure. Research has shown that the information obtained from

2D NMR spectra can frequently be fuzzy, contradictory, and incomplete7-10. These problems

primarily arise due to the presence of long-range 2D NMR correlations that span more than the

typical number of bonds allowed by the axioms outlined above (so-called nonstandard

correlations, NSC8) or severe overlap in the NMR spectra. Overlap leads to equivocal signal

assignments in the 2D spectra, and consequently to ambiguities in the spectral interpretations.

4

These possibilities mean that the initial axioms may fail (for instance, the hydrogen atom H(i) in

the real molecule is attached not to the carbon atom C(i) but to another carbon atom) and some

axioms can be violated (for instance, the topological distance between two HMBC correlated

atoms H(i) and C(j) is longer than three bonds (3JCH)).

To overcome these difficulties a human expert employs all of their knowledge, experience,

and intuition. One common approach is the suggestion of a structure for the unknown using a

series of similar molecules as a basis that have assigned chemical shifts both in 1H and 13C NMR

spectra. The comparison of the molecules with the proposed structure and its NMR spectra

allows chemical shift assignment that appears to be consistent with the suggested structure. The

correctness of the assignments is validated by checking the consistency of the chemical shifts

with the topological distances between the intervening atoms: an assignment is considered

acceptable if all distances are in agreement with the postulated axioms. The problem is reduced

to either confirming or refuting the proposed structure. Commonly some fragments of the

unknown compound can be inferred by the chemist through an understanding of the origin of the

sample (reactants, plant genus, etc.) and these fragments can also be utilized in the elucidation

process.

Data analysis can vary from simple to very complex depending on the nature of the

problem. For complex problems chemists can arrive at a structure for the unknown compound

that is incorrect. Our experience7-10 shows that CASE methods offer the possibility of

dramatically accelerating the process of structure elucidation and validation, as well as

increasing the reliability of the derived structure.

Expert systems now exist that are capable of modeling all stages of the structure

elucidation process via mathematical algorithms implemented in the corresponding software

programs. To date the most advanced CASE system is ACD/Structure Elucidator (StrucEluc)

which has been described in a large number of publications (for instance, 7,10-11). The StrucEluc

system mimics the sequence of steps performed by spectroscopists during the process of

5

structure elucidation. It should be noted that inside the program the structure elucidation process

is combined with structure verification in such a way that the structure verification procedure can

be carried out in an independent manner. StrucEluc is supplied with an extensive and branched

knowledgebase, sophisticated algorithms for inferring plausible structures from an initial set of

axioms, and a multiple algorithms for the accurate and rapid prediction of 1H, 13C, 15N, 19F, and
31
P nuclei. The efficiency of this system has been amply demonstrated by solving hundreds of

structural problems. Moreover, the application of StrucEluc allowed authors 12 to recognize the

structure of a complex natural product which had previously remained unsolvable by highly

qualified spectroscopists.

In this article we will demonstrate how the StrucEluc system can be applied to the

validation of different hypothetical structures derived by different researchers from the same

initial experimental data. For this aim, two important capabilities of StrucEluc were utilized: a)

the system makes it possible to follow the impact of how changes in the initial axioms influence

the inferred structures; b) the application of spectrum prediction for different proposed structures

allows comparison of different structural hypotheses and allows the choice of the most probable

structure(s).

This study was initiated by a discussion in the literature and on website blogs regarding the

complex chemical structure of a newly identified natural product named as hexacyclinol 14-16. The

essence of the problem will be explained in the next section.

2. The History of Hexacyclinol and Its Various Structural Forms

Hexacyclinol was first described by Gräfe and coworkers in 2002. 13 The compound was

isolated in Siberia from basidiospores collected from panus rudis strain HKI 0254. The

proposed structure (Figure 1a) contained a reactive epoxyketone and a highly strained

endoperoxide, which would be detrimental to the stability of the compound.

6

O
O

O O
O

O
O O
O

OH

OH
O O O
a b

Figure 1. Two conflicting hexacyclinol structures proposed by Gräfe et al.13 (a) and by
Rychnovsky15 (b).

The total synthesis of the structure proposed by Gräfe13 was first reported by La Clair in 2006. 14

The synthesis consisted of 37 steps, the final product being the molecule originally reported by

Gräfe.13 The synthetic scheme depicted by La Clair 14 included some difficult transformations,

such as a Mitsunobu inversion on a hindered alcohol. In addition, the amount of final product

reported (3.6 g) was unusually high for such a complex and lengthy scheme of reactions. It

seemed that this was an opportune time to reexamine the synthesis and structure of the molecule

in question.

The structure of hexacyclinol was revisited in an article by one of the authors,15 in which

other highly oxygenated and unsaturated molecules were compared with predictive NMR

calculations. When evaluating the chemical shift difference between calculated and

experimental hexacyclinol, it was found that the Gräfe13 structure of hexacyclinol had an

unusually high deviation, with an average of 6.8 ppm difference, and 5 carbon chemicals shifts

with more than a 10 ppm difference from the calculated structure. Using GIAO NMR

7

predictions, the structure of hexacyclinol was revised from the one proposed by Gräfe 13 to the

structure shown in Figure 1b.15

Following this, another of the authors performed a total synthesis of the revised structure

of hexacyclinol in order to determine the validity of the proposed structure.16 The molecule

proposed by Rychnovsky was indeed synthesized and the analytical data were identical to that

reported for natural hexacyclinol for 1H, 13
C and optical rotation studies. In addition, an X-ray

crystal structure was obtained, providing unequivocal structural confirmation. These data allow

for a thorough assessment of the power of CASE systems in elucidating heretofore unknown,

complex natural products

3. Structure Comparison Using ACD/Laboratories methods.

The initial question identified for investigation was assuming that the NMR data

obtained by Gräfe et al.13 are appropriately recorded and accurately reported. The NMR data

presented in the original publication are shown in Table 1. These data can be considered as

the initial set of spectral-structural axioms defining the given problem.

8

Table 1. NMR data utilized by Gräfe et al 13 for structure elucidation.

Positi C H COSY HMBC
on
1 18.6 1.77 s 142.2, 120.7
q
2 142.2
s
3 26.1 1,72 s 142.2, 120.7
q
4 120.7 4.82 d, 10.1 H-5
d
5 75.8 5.46 d, 10.1 H-4 60.5, 202.9
d
6 60.5
s
7 202.9
s
8 53.1 3.23 d, br, 3.5 H-9, H-10 202.9, 54.5
d
9 54.5 3.64 m H-8, H-10, H- 47.8
d 13
10 47.8 2.74, dd, 5.2, 7.8 H-9, H-11 54.5, 60.5
d
11 71.5 4.99 dd,5.2 br H-10, H-12
d
12 40.4 3.55 m H-11, H-13 61.0, 71.5, 72.7
d
13 72.7 3.8 dd, 9.5, 1.5, 2.54 br H-12, H-9 40.4, 54.5, 47.8, 53.1
d (OH)
14 61.0 3.51 dd, 2.9, 0.5 H-12, H-15 40.4
d
15 53.2 3.29 d, 3.2 H-14 132.5, 192.8
d
16 192.8
s
17 132.5
s
18 139.6 6.73 dd 5.3, 2.4 (allyl) H-19 192.8, 40.9
d
19 40.9 3.59 d, 5.3 H-18 139.6
d
20 77.3
s
21 26.6 1.26 s 77.3, 40.9
q
22 24.7 1.15 s 77.3, 40.9
q
23 49.1 3.02 s 77.3
q

9

The molecular formula, C23H28O7, and the spectral information from the 1H, 13
C,

COSY, HMQC, and HMBC data sets were manually input into the StrucEluc program. The

Molecular Connectivity Diagram (MCD)7-11 was created (Figure 2) using the criteria that

chemical bonds between oxygen atoms would be allowed but triple bonds are forbidden.

Using the most reliable multiplicities of the 1H NMR signals presented in Table 1 (where the

measured coupling constants coincide for intervening nuclei) the following numbers of

attached hydrogen atoms were set for specific carbon nuclei: 18.6 (0), 26.1(0), 120.7 (1),

75.8 (1), 47.8 (2), 139.6 (1), 40.9(1), 26.6(0), 24.7(0), 49.1(0). This additional structural

information significantly reduces the number of plausible structures. Note that the atom

properties and the number of attached hydrogen atoms displayed in the MCD complements

the system of axioms given in Table 1.

10

Figure 2. The Molecular Connectivity Diagram (MCD) created from the Gräfe data.13 The
atoms and their associated 13C chemical shifts and connectivities are displayed.
HMBC connectivities are marked by green connectivities while the COSY
connectivities are shown in blue. The atoms for which the hybridization type was set
to sp3 are marked in a blue color and the sp2 centers are colored in violet. The
contractions (fb) and (ob) mean that connections with heteroatoms are either
forbidden or obligatory.

According to the methodology of the StrucEluc application the MCD was checked for the

presence of contradictions using the usual of assumptions8 and the program reported that the

analyzed data were consistent. As has been reported elsewhere10 the most appropriate structure

generation fuzzy mode uses m=0-15, a=16, with generation stopped at m=mg. m is the number of

connectivities to be lengthened or removed and a is the number of bonds to be added to the

connectivity length (a=16 represents the removal of connectivities), mg is the m value at which

the resultant structural file is not empty. It is evident that if m=0 (when the data contain no

NSCs) then strict structure generation will be carried out. The fuzzy structure generation

procedure was initiated utilizing structural filtering via spectral libraries, the permanent

BADLIST (containing fragments which are unlikely in organic chemistry) and the checking of

chemical structures by Bredt’s rule. Four-membered rings were forbidden since these are

unlikely in natural products. These constraints accelerate the process of structure generation.

As a result of structure generation 5425 molecules were generated at mg=1 (denoted as
13
k=5425). The structure generation process took tg=56 sec. C chemical shift prediction was

carried out for all generated structures by both the incremental and the neural net approaches

using ACDCNMR Predictor17. The calculations consumed 66 sec. The resulting file was

reduced to 4961 structures after removal of duplicates (k=54254961). Structures containing the

O-OH group were filtered out since this fragment was deemed to be unlikely in natural products.

Excluding hydroperoxide moieties reduced the k value to 3097. According to the methodology

11

described earlier7,11 structures were ranked in order of the increasing deviation between the

experimental and calculated chemical shifts of the predicted structures. Four structures at the top

of the file ranked by the deviation of spectra calculated via increments dI(C) are shown in Figure

3.

Figure 3, displaying the COSY and HMBC connectivities, shows that Gräfe’s structure 13

(Figure 4) is the most probable structure when ranking is performed by dI(C). The next three

structures are very similar with Tanimoto structure similarity coefficients of 0.99, 0.99 and 0.97

and two of them are distinguished as preferable using other calculation approaches. The

deviations calculated for Gräfe’s structure are relatively large but when the complexity of the

structure is taken into account they are certainly acceptable.

All of these structures contain only one NSC (a=1) between the carbon resonances at 47.8

ppm and 53.1 ppm. The presence of at least one NSC is frequently observed for organic

molecules. Since the structures are both very similar and very complex, the applied methods of

chemical shift prediction cannot reliably prove or refute any of the structures. The results

obtained show that the structure suggested by Gräfe et al13 from the data displayed in Table 1

was also inferred by the CASE algorithms as one of the most probable. The location of the

structure proposed by Gräfe13 in the CASE output file should be considered as a consequence of

the total set of initial axioms and assumptions used by Gräfe, including the allowance of the

presence of one NSC and O-O bond in target structure.

12

1 (ID:515) 2 (ID:541)
Grafe's structure.
13
C incremental method.
H3 C
H3 C
O
O
O
O H3 C O
H3 C
O H3 C O
H3 C
OH
OH O H C
3
H3 C O
O CH3 O
CH 3 O

dA(13C): 5.071 (v.10.05) dA(13 C): 5.692 (v.10.05)
dI(13C): 3.808 dI(13C): 3.868
dN(13C): 4.130 dN(13C): 4.604
dA(1H): 0.434 (v.10.05) dA(1H): 0.423 (v.10.05)
dI(1H): 0.395 dI(1H): 0.380
dN(1H): 0.433 dN(1H): 0.424
dA Com plex : 8.462 dA Com plex : 8.842

3 (ID:1473) 13 4 (ID:520) 13
C HOSE, Complex, C neural nets
1
H neural nets.
CH3 H3C
H3 C H3C
O O
H3C H3C H3C
H3C

O
H3C
H3C
O O
O O
O
O
O
O

OH HO O
dA(13C ) : 4.584 (v.10.05) dA(13 C ) : 5.266 (v.10.05)
dI(13C): 4.238 dI(13C): 4.395
dN(13C): 5.042 dN(13C): 3.969
dA(1H): 0.366 (v.10.05) dA(1H): 0.404 (v.10.05)
dI(1H): 0.360 dI(1H): 0.431
dN(1H): 0.287 dN(1H): 0.444
dA Com plex : 7.916 dA Com plex : 8.413

Figure 3. The four structures at the beginning of the CASE structure elucidation output file
are ranked by the deviation of incrementally calculated spectra dI(C). The
inscriptions accompanying the structures list the type of spectrum prediction
method for which a given structure was ranked in first position.
13

26.10

18.60
142.20

26.60
120.70
O O
O 75.80
77.30 49.10

24.70
71.50 60.50 40.90

47.80

40.40 O 202.90
139.60
54.50
72.70 53.10
132.50

OH
61.00

192.80
53.20
O O

13
Figure 4. The structure of hexacyclinol proposed by Gräfe and the C chemical shift

assignment suggested his work13. The COSY (two-headed blue arrows) and HMBC

(unidirectional green arrows) connectivities are shown.

The number of NSCs in a structure has been shown to be very large as has been reported in

our earlier work.10 It is interesting to identify what type or types of structure(s) are generated if we

allow the presence of up to 4 NSCs in the analyzed structures as well as forbidding the peroxide

group as was suggested for Rychnovsky’s structure. 15 Setting a larger number of possible NSCs is

too time-consuming for this structural problem. Fuzzy structure generation was performed in the

secure mode {m=4, step by step, a=16}, implying that all m values between 0 and 4 will be taken

into account.10 To prevent the production of too large an output file incremental 13
C spectrum

14

prediction was performed during structure generation and only structures that had dI(13C) value

less than 4 ppm were saved to disk. The results obtained were as follows: 290141 molecules were

generated and 503 molecules were stored, removal of duplicates gave k=503386, and the process

was performed in a generation time of tg=16 m 42 s. All of the structures in the output file

contained two epoxy-containing cycles as represented in Rychnovsky’s structure. The “best”

structure (1) distinguished by the minimum sum of deviations D(sum)=dA(C) + dI(C) + dNet(C)

when the structures were ranked by the complex match factor dA( ) =dA(C)+dA(H) is shown below:

O
H 3C
O 53.10 18.60
202.90
47.80
54.50 60.50 142.20
CH 3
O 26.10
120.70
72.70 75.80 CH 3
71.50 26.60
77.30
139.60
O
HO 40.40 40.90
61.00 CH 3
132.50 CH 3
24.70 49.10

O
192.80

53.20
O

(1)

Four nonstandard COSY correlations are shown by the blue lines and one of them between the

proton bearing carbon atoms resonating at 40.40 and 61.00 ppm was unusually long, a 6JHH

coupling. There is no convincing explanation of why this coupling would exist. Comparison

between the deviations determined for Gräfe’s structure (Figure 4) and the structure (1) are given

in Table 2.

15

Table 2. The comparison of deviations calculated for structure 1 and for Gräfe’s structure (Figure

4).

Structure 1 Gräfe’s structure13
dA(13C) 3.808 dA(13C) 5.071
dI(13C) 2.873 dI(13C) 3.808
dN(13C) 2.564 dN(13C) 4.130
dA(1H) 0.412 dA(1H) 0.434
dI(1H) 0.420 dI(1H) 0.395
dN(1H) 0.356 dN(1H) 0.433
dA ( ) 6.126 dA ( ) 8.462

The table shows that, on one hand, the deviations found for structure (1) are markedly

smaller than Gräfe’s structure, but on the other hand four NSCs including one corresponding to a
6
JHH coupling appear in the structure. It is to be expected that further refining of the possible

structure by increasing the m value during fuzzy structure generation would result in further

violation of the initial axioms declaring that the lengths of the COSY and HMBC correlations

should be standard. The results obtained suggest that a revision of the initial data displayed in the

Table 1 may be necessary.

As mentioned earlier Rychnovsky15 suggested the hexacyclinol structure differing from

that suggested by Gräfe’s and offered chemical shift assignments for this newly suggested

structure using the spectral data published by Gräfe et al13. Deviations based on NMR

predictions were calculated for both structures suggested by Rychnovsky and Gräfe. The results

are listed in Table 3.

Table 3. A comparison of deviations for structures suggested by Gräfe and Rychnovsky
using the data listed in Table 1.

Gräfe’s structure13 Rychnovsky’s structure15
dA(13C) 5.071 dA(13C) 5.027
dI(13C) 3.808 dI(13C) 3.699
dN(13C) 4.130 dN(13C) 4.018
dA(1H) 0.434 dA(1H) 0.343
dI(1H) 0.395 dI(1H) 0.297
dN(1H) 0.433 dN(1H) 0.289
dA ( ) 8.462 dA ( ) 8.457

16

We see that all deviations calculated for the structure suggested by Rychnovsky are slightly

smaller than those for the structure suggested by Gräfe. However, checking Rychnovsky’s

structure relative to the 2D NMR data shows the presence of 12 NSCs with unusually long

topological distances between the intervening nuclei. Using a designation introduced

previously10, the set of NSCs can be symbolized as follows:

m=COSY{1a(5)+2a(4)+2a(3)+2a(2)}+HMBC {2a(5)+2a(4)+1a(3)} = 12,

where na(p) denotes that there are n connectivities that exceed by p bonds the standard length

assumed for a given 2D NMR technique (see Table 4). Rychnovsky’s structure with the

corresponding NSCs is shown below with the nonstandard connectivities marked by bold lines.

49.10

O
26.60 24.70 26.10
O
77.30
120.70 142.20
202.90

CH
40.90 75.80 18.60

HC 60.50
139.60
CH O
53.10
O
O 132.50 HC
47.80
CH
192.80 C 71.50
40.40 H
CH
54.50

53.20
HC
72.70
CH OH
61.00
O

2

17

49.10

O
26.60 24.70 26.10
O
C
77.30
HC 142.20
C 120.70
202.90
CH
40.90 CH 18.60
75.80
HC 60.50
139.60
CH O
53.10
O
O C CH
132.50 47.80
CH
C C 71.50
192.80 40.40
H CH
54.50

HC
53.20 HC
72.70
HC OH
61.00
O

2a

Table 4. Nonstandard connectivities present in the structure suggested by Rychnovsky

COSY HMBC
7
40.961.00 JHH 40.961.0 6JCH
6
40.972.7 JHH 40.972.7 5JCH
5
40.971.5 JHH 40.971.5 4JCH
4
40.4139.6 JHH 54.572.7 5JCH
6
72.754.5 JHH 53.172.7 6JCH
4
54.547.8 JHH
5
53.147.8 JHH

Analysis of the spectral data led Reynolds18 to conclude that the structure and NMR data

can be ratified to a larger extent if the 1H chemical shifts at 3.55 and 3.59 were exchanged. This

18

exchange only slightly reduced the deviations while the number of NSCs and their lengths still

remained fairly large (a=2-4). Up to this point in the present study attempts were made to resolve

the problem assuming that only the 2D NMR data of Gräfe13 was available and that the structure

suggested by Rychnovsky15 has chemical shift assignments based on these data.

The investigation led to the following conclusions: all possibilities to apply the 2D NMR

data published by Gräfe for clarifying the conflict between the two suggested structures were

exhausted and it was impossible to either prove or refute either of them. It became clear that

either the structure suggested by Rychnovsky was incorrect or that the chemical shift

assignments suggested in his work should be reexamined using new 2D NMR data.

Rychnovsky’s structure has been unambiguously confirmed by X-ray analysis16 so the challenge

remains in aligning the chemical shift assignments of the structure in agreement with all of the

NMR data.

4. NMR confirmation of the Rychnovsky structure

In order to determine appropriate chemical shift assignments for the Rychnovsky structure,

1D and 2D NMR spectra of the compound synthesized by Porco et al16 were acquired under

conditions described in the Experimental Section. Positions and numbers of resonances localized

in the strongly overlapped areas of 1H NMR were refined using 1H NMR spectrum registered at

the frequency of 900 MHz. Using ACD/SpecManager19 we automatically determined peak

positions, multiplicities, and coupling constants (when it was possible) in 1H spectrum. With

these data, assignments of series of peaks observed in 2D NMR spectra were revised. The

problem was reformulated in the following manner: once the structure is determined

unambiguously, determine those chemical shift assignments that remove the extremely long-

range correlations. Generally speaking, the criterion based on the minimization of the number of

NSCs and their length is of a heuristic nature, so this criterion should be added to the system of

axioms used for confirmation of the Rychnovsky structure.

19

To assist the process of understanding we will denote new experimental chemical shifts in

the 1H and 13
C NMR spectra using an italic font. The consideration of nonstandard

connectivities presented in both structures 2 and 2a shows that exchange of pairs of carbon atom

chemical shifts, specifically exchanging the pair 40.90(40.84) and 40.40(40.32) immediately

removes the nonstandard lengths of 3 of the unusually long HMBC connectivities: 40.90-71.50

(40.84-71.51), 40.90-72.70 (40.84-72.64) and 40.90-61.00 (40.84-60.94), This exchange of

assignments also adjusts the proton-proton connectivities in the COSY spectrum between the

protons attached to the following pairs of carbons: 40.90-71.50 (40.84-71.51), 40.90-72.70

(40.84-72.64), 40.90-61.00 (40.84-60.94) and 40.4-139.6 (40.32-139.70) to acceptable lengths

(3-4JHH). To edit the COSY (6JHH) and HMBC (5JCH) connectivities 72.70-54.50 (72.64-54.48) we

took into account that four 1H resonances 3.53, 3.61, 3.63 and 3.66 are observed in a very narrow

spectral interval (see Figure 5, where an expansion of the 1H NMR spectrum obtained at 900

MHz is displayed) related to several equivalent possibilities for HSQC peak assignment may be

expected. The 1H chemical shifts determined from this spectrum are very close to those found

from the HSQC spectrum. Assuming that 72.64(3.84) and 40.84(3.63) are newly assigned HSQC

assignments, then both the noted COSY and HMBC connectivities will assume standard lengths.

The 4JHH COSY connectivity 54.50-47.80 (54.48-47.71) is adjusted to a standard length when the

COSY correlation 3.66-2.76 is replaced by the correlation 3.63-2.76. The COSY peak 3.23-2.74

(53.10-47.8) shown in Table 1 might be assigned to a crosspeak 3.20-2.76 in the experimental

spectrum but careful analysis of the spectrum shows that this peak is absent from the 2D NMR

data and should be considered as an error. According to Table 1 the HMBC crosspeak at 54.50-

72.70 (54.48-72.64) is related to two peaks: 3.64-72.70 (3.66-72.64) and 3.80-54.50 (3.84-

54.48). Exchanging the assignments between 3.66 and the nearby shift of 3.63 leads to a 2JCH

correlation length. The HMBC peak 3.84-54.48 is not observed in the experimental spectrum.

The remaining long (6JCH) HMBC connectivity 53.10-72.70 (53.09-72.64) corresponds to the

20

13
crosspeak at 3.80-53.1 (3.84-53.09), and is transformed into a standard correlation when the C

NMR chemical shift 53.09 ppm is exchanged with the peak at 53.21 ppm.

Hexacyclinol Spectrum from Bruker_000000fid

7.5 7.0 6.5 6.0 5.5 5.0 4.5 4.0 3.5 3.0 2.5 2.0 1.5 1.0 0.5
Chemical Shif t (ppm)

Figure 5. An expansion of the 900 MHz 1H NMR spectrum

The final chemical shift assignment of the Rychnovsky15 structure is given in Table 5

where NMR data obtained in this work are shown in comparison with Gräfe’s data.13 The 13
C

and 1H chemical shifts determined in this work differ only very slightly from those determined in

the original work13. The near coincidence of the chemical shifts provides us with the basis to

conclude that the compound identified by Gräfe, et al13 had a structure consistent with that

suggested by Rychnovsky.15 This conclusion is further confirmed by the coincidence of

multiplicities and coupling constants in the 1H NMR spectra obtained by Gräfe et al.13 and in this

report.

The 13C and 1H chemical shift assignments are displayed on structure 3 below:

21

O
CH 3
(54.48)(3.66) (26.25)(1.73)

(71.51)(5.01) (53.09)(3.25)
OH 142.26
2.33
O
(120.67)(4.85) CH 3
(18.50)(1.79)
(75.74)(5.49)
(72.64)(3.84) (47.71)(2.76)
202.85
(60.94)(3.53) (40.84)(3.63) 60.40
O
O

(53.21)(3.32) 132.44 (40.32)(3.61)
CH 3
(24.69)(1.17)
192.75 (139.70)(6.76)

77.08

O
O
H 3C
(26.61)(1.28)
CH 3
(49.10)(3.04)

3

The COSY correlations accompanied by the peak multiplicities and the measured coupling

constants are shown on structure 3a:

H3C
3.04
O
H3 C CH 3 CH 3
1.17 1.28
O 1.73
m
4.85
dd,5.37, 3.11

3.61
5.49 d, 9.04
6.76 CH 3
dd, 5.65, 2.54
3.25 1.79
d, 3.67 O
O
O 2.76 dd, 10.31, 5.23
5.01 dd, 5.1, 3.67
3.63 3.66
tt, 9.9, 2.7
t, 3.53

3.32 d, 3.4 3.84 d, 9.61

3.53 OH
O
d, 3.4 2.33

3a

22

When the new NMR data presented in Table 5 were entered into the Structure Elucidator

program only three structures were produced in 0.095 s. After selection of the best structure, the

program placed structure 3 at the first position and with the same 1H and 13C assignments shown.

Table 6 lists the deviations calculated for the Rychnovsky15 structure both with the old (see

Table 3) and the new assignments.

Table 6. A comparison of the deviations calculated for the Rychnovsky structure with both

old and new chemical shift assignments. All entries are on ppm.

Old assignment New assignment
dA(13C) 5.03 dA(13C) 4.46
dI(13C) 3.70 dI(13C) 3.07
dN(13C) 4.02 dN(13C) 2.60
dA(1H) 0.34 dA(1H) 0.33
dI(1H) 0.30 dI(1H) 0.29
dN(1H) 0.29 dN(1H) 0.28
dA ( ) 8.46 dA ( ) 5.40

It is evident that the deviations calculated by all methods are smaller for the structure for

which chemical shifts were assigned in this work. Note that all 2D NMR correlations in the

structure 3 are now of standard length.

5. Experimental section.

All of the 900 MHz NMR data was obtained on a Bruker AVANCE-900 NMR

spectrometer which was equipped with a Bruker 5-mm TCI cryoprobe. A synthetic sample (+)-

Hexacyclinol (~1.2 mg ) was dissolved in ~120 uL CDCl3, contained in a 3-mm o.d. NMR

sample tube (~ 3-cm sample height) and centered in the receiver coil of the cryoprobe. 1H NMR

spectra were acquired with 64 K data points and zero-filled to 256 K data points prior to Fourier

transformation. All 2-D experiments (gCOSY, gHSQC, gHMBC) employed gradient-enhanced

pulse sequence versions and were acquired with proton detection in f2. The gCOSY data was

acquired with 2 K points in f2 with 256 increments in f1. The f1 increments were linear

23

predicted to 2k and both f1 and f2 were zerofilled to 4k points to yield a 4k x 4k data set after

Fourier transformation. The gHSQC and gHMBC experiments were acquired with 2k points in

f2 and 128 increments in f1 (gHSQC) and 256 increments in f1 (gHMBC) and subsequently

linear predicted to 1k increments and 2k increments in f1, zerofilled to 4k x 2k (gHSQC) and 4k

x 4k (gHMBC), respectivel, prior to Fourier transformation. The frequency range of the carbon-

13 sweep widths for the gHSQC and gHMBC experiments was 180 and 220 MHz, respectively.

6. Conclusions.

It is rather an uncommon situation when different research groups publish different

chemical structures for newly separated or synthesized organic molecules, especially when 2D

NMR data are used for the structure elucidation. This is more likely to happen if there is severe

overlap in the NMR spectra since this eventuality leads to ambiguous interpretation of the data.

With severe overlap in the proton spectrum incorrect chemical shift assignments can carry

through the homonuclear and heteronuclear HSQC (HMQC) spectra. If two researchers employ

slightly different initial data then it is possible that they can arrive at different structures. In this

article, we have demonstrated that resolving contradiction(s) between two or more proposed

structures the capabilities within the expert system Structure Elucidator7-10 can be extremely

advantageous since the system is capable of both generating and validating different structural

solutions derived from the data.

The system was applied to the selection of the most appropriate structure from two

suggested variants of the natural product hexacyclinol. This structure was first separated and

structurally characterized by Gräfe et al13. In the next works15-16 the structure of hexacyclinol

was revised and an alternative structure was confirmed via synthesis and X-ray analysis.

Combining the procedures of both structure generation and spectrum prediction incorporated into

the expert system we checked both structural hypotheses and independently confirmed the

revised structure.

24

In order to help in a fresh analysis of the NMR data we reacquired 1D and 2D spectra at a

proton NMR frequency of 900 MHz for a sample of the synthesized compound as described

elsewhere16. With these data we have been able to reassign both the 1H and 13C chemical shifts.

The reassignment was governed by the heuristic requirement of eliminating unusually long

COSY and HMBC correlations. As a result a number of the chemical shift pairs with very

similar chemical shifts were permuted and all 2D NMR connectivities were converted to

standard lengths. Simultaneously, the chemical shift deviations calculated by all available

prediction methods were smaller than those suggested by Rychnovsky, thereby endorsing the

new assignment. A number of the exchanged chemical shifts are actually very close and the

criterion of minimizing the number of non-standard correlations is heuristic in nature and leads

to the question: is the suggested assignment correct? Turning to the works of Sigmund Freud20

we quote: “An attribute of scientific thinking is the possibility to be content with an

approximation to the truth and to continue creative work in spite of the absence of final

confirmation”. We have no further data available to us to assist in checking the suggested

assignment so we accept the conclusions as being accurate and appropriate.

25

REFERENCES

1. Lederberg, J.; Sutherland, G.L.; Buchanan, B.G.; Feigenbaum, E.A.; Robertson, A.V.;

Duffield, A.M.; Djerassi, C. J. Am. Chem. Soc. 1968, 91, 2973-2976.

2. Elyashberg, M.E.; Gribov, L.A. Zh. Prikl. Spectros. 1968, 8, 296-300.

3. Sasaki, S.I.; Abe, H.; Ouki, T.; Sakamoto, M.; Ochiai, S. Anal.Chem. 1968, 40, 2220-

2223.

4. Nelson, D.B.; Munk, M.E.; Gasli, K.B.; Horald, D.L. J. Org. Chem. 1969, 34, 3800-

3805.

5. Elyashberg, M.E.; Gribov, L.A.; Serov. V.V. Molecular Spectral Analysis and Computer

(in Russian), Nauka, Moscow, 1980.

6. Elyashberg, M.E.; Martirosian, E.R; Karasev, Yu.Z.; Thiele, H.; Somberg, H. Anal.

Chim. Acta. 1997, 348, 443-463.

7. Elyashberg, M. E.; Blinov, K. A.; Molodtsov, S. G; Williams, A. J.; Martin, G. E. J.

Chem. Inf. Comput. Sci. 2004, 44, 771-792.

8. Molodtsov, S.G.; Elyashberg, M.E.; Blinov, K.A., Williams, A.J.; Martin G.E., Lefebvre,

B. J. Chem. Inf. Comput. Sci. 2004, 44, 1737-1751.

9. Elyashberg, M. E.; Blinov, K. A.; Molodtsov, S. G; Williams, A. J.; Martin, G.E.

J. Chem. Inform. Model. 2006, 46, 1643-1656.

10. Elyashberg, M. E.; Blinov, K. A.; Molodtsov, S. G; Williams, A. J.; Martin, G. E.

J. Chem. Inform. Model. 2007, 47, 1053-1066.

11. Blinov, K. A.; Carlson, D.; Elyashberg, M. E.; Martin G. E.; Martirosian, E. R.;

Molodtsov, Molodtsov, S. G.; Williams. A. J. Magn. Reson. Chem. 2003, 41, 359-372.

12. Blinov, K.A.; Elyashberg, M.E.; Martirosian, E.R.; Molodtsov, S.G.; Williams, A. J.;

Sharaf, M. M. H.; Schiff, P. L. Jr.; Crouch, R.C.; Martin, G. E.; Hadden, C.E.; Guido

J.E.; Mills, K.A. Magn. Reson. Chem. 2003, 41, 577-584.

26

13. Schlegel, B.; Härtl, A.; Dahse, H.-M.; Gollmick, F. A.; Gräfe, U.; Dörfelt, H.; Kappes,

B. J. Antibiot. 2002, 55, 814-817.

14. La Clair, J.J. Angew. Chem. Int. Ed. 2006, 45, 2769–2773.

15. Rychnovsky, S. D. Org. Lett. 2006, 8, 2895-2898.

16. Porco, Jr., J.A.; Su, S. ; Lei, X.; Bardhan, S.; Rychnovsky, S. D. Angew. Chem. Int. Ed.

2006, 45, 1–4.

17. ACD/CNMR Predictor v.10.0. Advanced Chemistry Development Inc., 110 Yonge

Street, 14th floor, Toronto, Ontario, Canada M5C 1T4.

18. W.F. Reynolds. SMASH-2006.

19. ACD/SpecManager v.10.0. Advanced Chemistry Development Inc., 110 Yonge

Street, 14th floor, Toronto, Ontario, Canada M5C 1T4.

20. S. Freud. New introductory lectures on psycho-analysis. London, 1933.

27

Applying Computer Assisted Structure Elucidation Algorithms For The Purpose Of Structure Validation – Revisiting The NMR Assignments Of Hexacyclinol

More Related Content

What's hot (15)

Viewers also liked (11)

Similar to Applying Computer Assisted Structure Elucidation Algorithms For The Purpose Of Structure Validation – Revisiting The NMR Assignments Of Hexacyclinol (20)

Recently uploaded (20)

Applying Computer Assisted Structure Elucidation Algorithms For The Purpose Of Structure Validation – Revisiting The NMR Assignments Of Hexacyclinol