Guido F Pauli1, Matthias Niemitz2, Jonathan Bisson1, Michael W Lodewyk3, Cristian Soldi4,5, Jared T Shaw4, Dean J Tantillo4, Jordy M Saya6, Klaas Vos6, Roel A Kleinnijenhuis6, Henk Hiemstra6, Shao-Nong Chen1, James B McAlpine1, David C Lankin1, J Brent Friesen7. 1. Department of Medicinal Chemistry & Pharmacognosy and Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago , 833 South Wood Street, Chicago, Illinois 60612, United States. 2. PERCH Solutions Limited , Puijonkatu 24B5, 70110 Kuopio, Finland. 3. Physical Science Department, Butte College , Oroville, California 95965, United States. 4. Department of Chemistry, University of California-Davis , One Shields Avenue, Davis, California 95616, United States. 5. Federal University of Santa Catarina , Centro de Curitibanos, Rod. Ulysses Gaboardi, Km 3, Curitibanos, SC 89520-000, Brazil. 6. Van't Hoff Institute for Molecular Sciences, University of Amsterdam , Science Park 904, 1098 XH Amsterdam, The Netherlands. 7. Physical Sciences Department, Rosary College of Arts and Sciences, Dominican University , 7900 West Division Street, River Forest, Illinois 60305, United States.
Abstract
The revision of the structure of the sesquiterpene aquatolide from a bicyclo[2.2.0]hexane to a bicyclo[2.1.1]hexane structure using compelling NMR data, X-ray crystallography, and the recent confirmation via full synthesis exemplify that the achievement of "structural correctness" depends on the completeness of the experimental evidence. Archived FIDs and newly acquired aquatolide spectra demonstrate that archiving and rigorous interpretation of 1D (1)H NMR data may enhance the reproducibility of (bio)chemical research and curb the growing trend of structural misassignments. Despite being the most accessible NMR experiment, 1D (1)H spectra encode a wealth of information about bonds and molecular geometry that may be fully mined by (1)H iterative full spin analysis (HiFSA). Fully characterized 1D (1)H spectra are unideterminant for a given structure. The corresponding FIDs may be readily submitted with publications and collected in databases. Proton NMR spectra are indispensable for structural characterization even in conjunction with 2D data. Quantum interaction and linkage tables (QuILTs) are introduced for a more intuitive visualization of 1D J-coupling relationships, NOESY correlations, and heteronuclear experiments. Overall, this study represents a significant contribution to best practices in NMR-based structural analysis and dereplication.
The revision of the structure of the sesquiterpeneaquatolide from a bicyclo[2.2.0]hexane to a bicyclo[2.1.1]hexane structure using compelling NMR data, X-ray crystallography, and the recent confirmation via full synthesis exemplify that the achievement of "structural correctness" depends on the completeness of the experimental evidence. Archived FIDs and newly acquired aquatolide spectra demonstrate that archiving and rigorous interpretation of 1D (1)H NMR data may enhance the reproducibility of (bio)chemical research and curb the growing trend of structural misassignments. Despite being the most accessible NMR experiment, 1D (1)H spectra encode a wealth of information about bonds and molecular geometry that may be fully mined by (1)H iterative full spin analysis (HiFSA). Fully characterized 1D (1)H spectra are unideterminant for a given structure. The corresponding FIDs may be readily submitted with publications and collected in databases. Proton NMR spectra are indispensable for structural characterization even in conjunction with 2D data. Quantum interaction and linkage tables (QuILTs) are introduced for a more intuitive visualization of 1D J-coupling relationships, NOESY correlations, and heteronuclear experiments. Overall, this study represents a significant contribution to best practices in NMR-based structural analysis and dereplication.
Despite major advances
in analytical spectroscopy, structural elucidation
of both natural and synthetic compounds continues to be a major challenge,
as is illustrated by the recent revision of the structure of aquatolide
(1a/1b), a natural product isolated from Asteriscus aquaticus. Initially reported as containing a
bicyclo[2.2.0]hexane core substructure, 1a (Figure ),[1] upon subsequent re-examination of the spectroscopic data,
indicated the structure to be more consistent with bicyclo[2.1.1]hexane 1b.[2] This structural revision was
supported by a detailed NMR analysis spurred on by quantum chemical
calculations and confirmed through X-ray crystallography.
Figure 1
Originally proposed (1a)
and revised structure (1b) of aquatolide.
The
problem of misassigned spectra ultimately leading to incorrect
structural assignments is becoming a more prevalent feature in the
contemporary chemical literature with no apparent signs of abating.[3−7] In fact, there have been in excess of 160 articles describing structural
revisions of organic molecules, predominately as a result of spectral
misassignment, in the decade since Nicolaou and Snyder published their
comprehensive review in 2005[8] on misassigned
structures as revealed by chemical synthesis.To curb the growing
trend of reported misassigned structures, we
propose an approach that better utilizes the vast structural information
contained in the ubiquitously acquired 1D1H NMR data sets
with the purpose of achieving “structural correctness”
while at the same time enhancing the reproducibility of downstream
research performed with the structurally correct compound in question.
The present study demonstrates that practically everything the chemist
needs to know for a correct structural elucidation process is contained
in the proton NMR FIDs. Our proposed protocol involves analysis of
1D1H spectra including both quantum-mechanical prediction
of chemical shifts (δ) and scalar coupling constants (J) as well as extraction of compound-specific 1H NMR spectral parameters from the experimental data. Although even
classical manual analysis of the spectra is capable of providing sufficient
information to verify (or revise) a structure, we demonstrate here
that an iterative fitting process utilizing quantum mechanical spin
information (HiFSA)[9] is indispensable for
achieving rigorous structural elucidation and dereplication with a
high degree of reproducibility.To preserve the authenticity
of reported spectral information,
originally acquired free induction decays (FIDs) should be made available
for published structures.[10] The approach
described here is applied to aquatolide by analysis of the published
data together with a reprocessing and HiFSA fitting of the 1H FID that was archived in 2012 and provided by the authors of the
revision article.[2] A thorough analysis
of the data revealed the dangers and pitfalls of a superficial treatment
of 1D NMR spectroscopic data and will hopefully serve as a future
guide for avoiding similar spectral misinterpretations, including
deduction of newly discovered structures that were not there initially.[8]
Results and Discussion
Chemical Shift Plausibility
The key to both the suitability
of a proposed structure, or guidance for its revision, may be found
in the 1D1H and 13C NMR spectra. In the case
of aquatolide, the suspect structure 1a was recently
evaluated by comparing the experimental data with that of the 13C and 1H chemical shifts predicted with quantum
chemical calculations. Significant deviations (ΔδC) of up to 24.33 ppm in the 13C domain indicated
a potential problem with the originally assigned structure. Over 60
alternative scaffolds, along with their diastereomers, were generated
by both rational and arbitrary changes to the original structure.
One alternative structure, 1b (originally suggested by
P.B. Jones), yielded a much better predictive fit than the original
structure with the largest ΔδC of 4.28 ppm.
The prediction of the 1H NMR chemical shifts of aquatolide
demonstrated much the same trend as the 13C study. The
revised structure, 1b, exhibited a better fit (largest
ΔδH = 0.27 ppm) than the original structure
with the largest ΔδH = 1.31 ppm. Although deviations
of such magnitude are widely accepted as representing a reasonable
gap between theoretical or empirical predictions and experimental
observations,[11,12] it is also well-known that nearly
identical yet different molecules can exhibit very minute chemical
shift differences in the range of up to a few hundred ppb in 13C and only a few tenths to sub ppb level in 1H
NMR spectra.[13,14] This obvious contradiction provides
a rationale for the need to perform comprehensive mining of 1D NMR
data in general structure analysis.Originally proposed (1a)
and revised structure (1b) of aquatolide.
Correlation Maps Visualize Coupling Networks
In the
structural revision, the evaluation of 1H coupling constants
and multiplicities faced the challenge of a lack of comparison due
to the meager information content in the original reference article.[1] The quantity of coupling information obscured
by multiplets in the original article can be demonstrated by compiling
the reported couplings into a J-correlation map: Figure A graphs all possible
scalar coupling combinations present in the molecule in the lower
left half,[2] whereas the corresponding number
of bonds between coupled nuclei are given in the upper right half.
The map demonstrates the inherent risk associated with the reporting
of “multiplets.” For example, only three couplings were
reported mutually for the pair of coupled nuclei (3JH-1,H-2, 4JH-1,H-10, 3JH-2,H-10) and only one of the two couplings
(2JH-4a,H-4b, 3JH-4a,H-5b), as
indicated by the divided cells in Figure A. Ignoring characteristic long-range couplings
(4–5J), only six out of a total
of 22 values that reflect the pairwise relationship of all possible 3J and 2J couplings
were reported. The unreported 2J and 3J couplings were obscured by “multiplets”
or simply not observed. A 4J coupling
of 1.9 Hz was proposed for nuclei H-1 and H-10, but neither the observed
nor the conspicuously unobserved couplings were actually discussed
in the original article.
Figure 2
J-correlation
map of the homonuclear proton NMR
assignments reported for the original (erroneous) A and
revised B structures of aquatolide (δ in ppm, M
= reported multiplicity). Cells in the upper right are the number
of bonds separating the two hydrogens. In the lower left are the observed
coupling constants in Hz. Unresolved multiplets were designated by
“m.” ø are 3J coupling
constants that are less than 1.0 Hz due to ∼90 deg dihedral
relationships. The addition of “a” in the bond numbers
4a and 5a indicate (homo)allylic coupling relationships. Split cells
in the lower left represent coupling constants that are unequally
reported for the two nuclei, likely referring to observed line distances
rather than coupling constants. Yellow boxes in B indicate
changes in bond number compared with the original structure.
Consequences of Incomplete Correlation Maps
The apparent
lack of attentiveness to coupling patterns and coupling constants
exposes a general attitude that 1D proton NMR data is both uninterpretable,
at least in great parts, and inferior to that of many 2D experiments.
Unfortunately, this lack of attention to 1H NMR spectra
(the “mother of all NMR experiments”) is very common
in both the natural product structural elucidation literature and
reports on the structural characterization of synthetic compounds.
In the case of aquatolide, the original authors were likely led astray
by resorting to the all-too-common practice of moving on to the 2D
data without thoroughly understanding the 1D data. Moreover, Lodewyk
et al. deemed the existing 2D data incapable of definitively verifying
the revised structure.[2] Thus, the compound
was reisolated from Asteriscus aquaticus, and an
NMR analysis was performed at 800 MHz. It is reasonable to assume
that the two isolates yielded the same compound despite the lack of
reference material from the original work because the 1H and 13C data sets appear to be very similar. A detailed
analysis of the proton data was performed after reisolation. The progress
achieved with the revision[2] is illustrated
in the J-coupling correlation map in Figure B, showing the reported experimental
values for the revised aquatolide structure. In this case, five out
of 18 3J couplings and one out of four 2J couplings were observed. Interestingly,
five 4J and two 5J long-range couplings were observed due to the rigid ring structure
and presence of an α,β unsaturated ketone.Although
the NMR results in the 2012 study represented a substantial qualitative
improvement over the data reported in the original article,[1] a different overall focus and approach did not
lead to an exhaustive description of the chemical shifts (δ)
and scalar coupling constants (J) present in this
molecule by resolving highly complex 1H NMR signal patterns.
In fact, a thorough treatment of all relevant 1D and 2D NMR data is
generally discouraged by current journal practices, relegating in
the best case such critical NMR information to the Supporting Information.
These practices only serve to reinforce the myth that 1H NMR data is both ambiguous and inferior to 2D NMR data.In
the revision,[2] the use of quantum
chemical prediction tools for evaluating the observed scalar coupling
network led to a complete, yet theoretical, J-correlation
map (Supporting Information, Figure S1).[15] The
predictive exercise proposed 14 coupling constants above 1.0 Hz, of
which ten were observed for at least one proton. Notably, the prediction
confirmed several instances of unusual coupling behavior, including
the unobservable to 3JH-2,H-9 and 3JH-9, H-10 couplings
with near zero values.However, several challenges remained
for a comprehensive representation
of the coupling network: (i) the magnitude of the coupling constants
obscured by multiplets cannot be confirmed or unconfirmed; (ii) four
of the observed coupling constants exhibit deviations of 0.5–0.8
Hz from the predicted values; (iii) the relative positions of protons
4a, 4b, 5a, and 5b could not be determined with certainty due to the
ambiguity of matching all of their exact chemical shifts; (iv) two 3J coupling constants are nearly undetectable
(<1.0 Hz), whereas five 4J and 5J long-range coupling constants are >1.0
Hz, the origin of which requires a closer examination.J-correlation
map of the homonuclear proton NMR
assignments reported for the original (erroneous) A and
revised B structures of aquatolide (δ in ppm, M
= reported multiplicity). Cells in the upper right are the number
of bonds separating the two hydrogens. In the lower left are the observed
coupling constants in Hz. Unresolved multiplets were designated by
“m.” ø are 3J coupling
constants that are less than 1.0 Hz due to ∼90 deg dihedral
relationships. The addition of “a” in the bond numbers
4a and 5a indicate (homo)allylic coupling relationships. Split cells
in the lower left represent coupling constants that are unequally
reported for the two nuclei, likely referring to observed line distances
rather than coupling constants. Yellow boxes in B indicate
changes in bond number compared with the original structure.
Raw NMR Data (FIDs) Enable
Multiplet Analysis
Data
produced by modern FT-based NMR experiments are time domain data,
free induction decays (FIDs) or series thereof, which are stored,
processed, and handled digitally. FIDs are relatively small files,
machine and vendor specific, but in relatively transparent file formats,
and importantly are easy to archive. Commercial as well as free software
tools are available for (re)processing FIDs (see, e.g., http://nmr-software.blogspot.com/ for a listing and links). Moreover, the resolution of multiplets
may be achieved, in many cases, by optimizing post-acquisition data
processing parameters.The present study became possible because
the 1H FID of the newly isolated aquatolide (1b) was archived and accessible via the authors.[2] Thus, the 800 MHz 1H FID could be reprocessed
with resolution enhancement (e.g., Lorentzian–Gaussian apodization)
to resolve even very small coupling constants (∼1.0 Hz) as
line splittings in all signals. Manual spectral interpretation of
an optimized spectrum led to a more complete J-correlation
map (Figure A), showing
that “multiplets” may be tentatively resolved through
optimized processing of FIDs and no additional experiments. Visual
interpretation of the resulting highly resolved multiplets may be
facilitated by software tools, such as Schimanski’s jVisualizer
(http://jvisualizer.sourceforge.net/), to help simulate
the line patterns of manifold-coupled resonances using first order
assumptions. In most cases, the manually extracted J-couplings matched up well (within 1 Hz, often much better) with
the predicted values (Figure ). It is noteworthy to mention that strong apodization for
very strongly enhanced resolution can affect both the exact line distances
as well as the relative intensities of individual lines within resonances
and of resonances relative to each other. Accordingly, HiFSA processing
typically uses spectra that are not or only weakly apodized.
Figure 3
(A) Results
of reprocessing the FID from the 800 MHz 1D 1H NMR spectrum
of aquatolide displayed on a J correlation
map. The number of bonds separating two coupled nuclei are color-coded:
violet = 2J, blue = 3J, yellow = 4J, green = 5J, and pink = 6J. The gaps in the colored fields of the lower left indicate the limitation
of achievable coverage with manual spin analysis. Whereas all couplings
of ∼1 Hz or more could be readily extracted, determination
of the long-range J-couplings typically requires
a computational approach. (B) Final J-correlation
map, termed quantum interaction and linkage table (QuILT; see main
text), achieved by HiFSA fitting of the archived 800 MHz 1D 1H NMR data of aquatolide. Multiplicities in parentheses are less
than ∼1 Hz. Couplings less than absolute value of 0.10 Hz are
given as “⌀” rather than being reported as blank
cells, which would indicate them being unknown or undetermined.
(A) Results
of reprocessing the FID from the 800 MHz 1D1H NMR spectrum
of aquatolide displayed on a J correlation
map. The number of bonds separating two coupled nuclei are color-coded:
violet = 2J, blue = 3J, yellow = 4J, green = 5J, and pink = 6J. The gaps in the colored fields of the lower left indicate the limitation
of achievable coverage with manual spin analysis. Whereas all couplings
of ∼1 Hz or more could be readily extracted, determination
of the long-range J-couplings typically requires
a computational approach. (B) Final J-correlation
map, termed quantum interaction and linkage table (QuILT; see main
text), achieved by HiFSA fitting of the archived 800 MHz 1D1H NMR data of aquatolide. Multiplicities in parentheses are less
than ∼1 Hz. Couplings less than absolute value of 0.10 Hz are
given as “⌀” rather than being reported as blank
cells, which would indicate them being unknown or undetermined.Introduction of color coding to
the J-correlation
map in Figure A visually
connects the two near symmetric halves of the J-correlation
map, i.e., connecting bonds and coupling constant(s). This facilitates
two important elements of 1D1H NMR interpretation: (a)
verification of all coupling constants that should be present due
to geminal (2J) and vicinal (3J) relationships with the notable exception of couplings
that are (near) zero due to (near) perpendicular dihedral bond angles;
and (b) detection of long-range couplings (≥4J) that are characteristic for the given structure, such
as aromatic, allylic, homoallylic, and W-type couplings. Although
these couplings are often small (up to ∼3 Hz), they can reach
values of >10 Hz under certain circumstances, such as the 2-fold
W-type
coupling pathway that is present in compound 1b showing
a 7.2 Hz 4JH-2,H-10. Accordingly, it is important to keep in mind that, in the same
molecule, geminal and vicinal J values can be smaller
than long-range J values and potentially generate
confusion in the early interpretation process. Again, 1b is a perfect example of such a situation as two 3J couplings are near zero, whereas five long-range couplings
lead to signal splittings in the 1.5–7.2 Hz range.
HiFSA Enables
Quantum Interaction and Linkage Tables (QuILTS)
The aforementioned
data processing and prediction methodologies
will likely still exhibit gaps between observed and predicted values.
Naturally, these must be investigated and resolved to fully confirm
the structure and utilize the information contained in the data. The
HiFSA technique iteratively fits, within the limits allowed by the
conformation and quantum mechanical parameters, the predicted values
into the observed spectrum[9] to create a
high resolution data set that completely defines the J-coupling network (see ref (16) for a discussion of δ and J precision).
This enables completion of the J-correlation map,
creating a quantum interaction and linkage table (QuILT). This comprehensive
approach allows the researcher to analyze a definitive homonuclear
data set to base structural assignments on the most definite information
that can be derived from the data.
Intelligent Use of HNMR
Observations
Even in the case
of nearly matching theoretical and observable data, the final values
need to be correlated with known NMR results and the structural features
of the molecule. This is a process that cannot be completely automated
and requires the intervention of a knowledgeable spectroscopist. Whereas
every shift and coupling constant computed with quantum mechanical
calculations (for a review, see ref (11)) is associated with a specific structural feature,
a frequent issue is merely whether these values are predicted with
high enough accuracy to assign experimental values that are very close
to each other unambiguously.In the case of aquatolide, a 4J constant greater than 7 Hz is certainly
worthy of closer inspection, as are two 3J values of nearly zero, all occurring in the same molecule of only
15 carbons. Ideally, all observed and potentially observable J-couplings should be verified by considering the impact
of geometries, such as the phenomena associated with strained rings
and allylic and homoallylic relationships.Another role for
the HiFSA process, which involves the prediction
of spin parameters from energy-minimized structures as starting values
for the iteration,[9] is the use of the chemical
shift and J-coupling predictions to distinguish between
the two structures. As shown in Figure A, significant differences exist between both proposed
structures and the actual (fitted) values, especially in the bicyclic
ring structure involving protons H-1, H-2, H-9, and H-10. The average
difference of chemical shifts (Δδ) in the final HiFSA
profile favors the revised structure, 0.3060 ppm compared to 0.3990
ppm for the original structure. However, this comparison alone is
not conclusive as the chemical shift prediction algorithms are not
yet mature enough to distinguish between the near-identical molecules, 1a/1b.
Figure 4
Difference of chemical
shifts (in ppm, A) and coupling
constants (in Hz, B) between the HiFSA fitted structure
and the original vs revised structures.
In contrast, comparison of the coupling
constants in Figure B shows that the revised structure
exhibits a better fit, especially in the bicyclic ring structure.
Although the average difference (ΔJ) across
all 28 coupling constants of 1.643 Hz already favors the revised structure
compared to 2.063 Hz for the original structure (ΔΔJ = 0.420 Hz), Figure B shows that four individual coupling constants exhibit
major differences with a total ΔJ of 14.551
Hz (average of 3.638 Hz). The four critical spots of J pattern interpretation are as follows. (i) The magnitude of the 3JH-1,H-2 for a dihedral relationship
of ∼ 0° in 1a would be more in line with
a value of ∼9 Hz, contrasting the 2.502 Hz measured. (ii) In
cyclobutane relationships, the coupling between H-2 and H-9 cannot
be neglected, especially not a 4J as present in 1a, which
are known to give rise to coupling constants of up to −3 Hz;[17] the revised interpretation as a 3J of 0.513 Hz in 1b demonstrates how
potentially misleading the (apparent) lack of coupling can be. (iii)
Representing the cyclobutane form of a 2-fold “W” or
“4J” coupling, known to reach up to 18 Hz,[18] the 4JH-1,H-10 relationship
would be expected to be much larger in the original structure, 1a. (iv) The 3JH-2,H-10 relationship would be expected to be ∼2 Hz larger than was
measured. Considering that couplings are related to structure, geometry,
and bonding, it is important to keep in mind that both the absolute
differences and the signs of the coupling constants are diagnostic
and indicative of the correct structure.Difference of chemical
shifts (in ppm, A) and coupling
constants (in Hz, B) between the HiFSA fitted structure
and the original vs revised structures.
Full HNMR Interpretation of Aquatolide (1b)
The following analysis provides a model treatment of 1H homonuclear NMR data, which should be reported for even apparently
straightforward structural assignments. Confirmation employing 2D
data sets is appropriate after the 1D spectrum has been thoroughly
examined and can focus on issues that are otherwise not fully resolved.
Bicyclo[2.1.1]hexane
Core Protons
H-1 is the only proton
on the two-carbon bridge of the bicyclo[2.1.1]hexane core of 1b. The chemical shift of this signal is at δ 4.4797
ppm because it is deshielded by the adjacent lactonic alkyl oxygen.
The signal was reported as a dd in the original article and as a triplet
in the revision article. The 3J coupling
with H-2 (2.502 Hz) at the closest bicyclo[2.1.1]hexane bridgehead
is clearly observed but rather small due the 50° dihedral angle.
A 4J (by two pathways) coupling of 1.839
Hz is observed with H-10, the remote bicyclo[2.1.1]hexane bridgehead
proton. The occurrence of 4J couplings
in strained rigid ring systems has been previously described[19,20] and exemplifies the significance of long-range couplings in general.[21] The original aquatolide structure also placed
H-1 at a position where it was three bonds away from H-2 and four
bonds away from H-10. However, in the original structure, the dihedral
angle between H-1 and H-2 approaches 0°.Proton H-2 occupies
a bridgehead position of the bicyclo[2.1.1]hexane core of 1b. The chemical shift of its dd signal is at δ 3.2598 ppm, making
it the third most downfield proton in this molecule. Interestingly,
the 3J coupling with H-9 on the cyclobutane
ring is not observed. The quantum chemical calculations put the coupling
constant at less than 0.5 Hz (predicted at −0.119 Hz), which
is due to a nearly 90° dihedral angle. The 4JH-2,H-10 coupling (by two routes)
on the two bridgehead carbons is a remarkable 7.219 Hz. This is remarkably
large for a saturated 4J coupling. However,
this value may be predicted (HiFSA processing predicted 6.299 Hz,
the quantum mechanical calculations yielded 6.767 Hz) and has been
observed in other cyclobutanes[22] as well
as in bicyclo[2.1.1]hexane derivatives.[19] The magnitude of this coupling may be attributed to the rigid W
conformation present in the molecule and the fact that there are two
parallel 4J coupling pathways. Notably,
the H-2 coupling pattern and J values are very likely
the explanation as to why, in the original aquatolide structure, protons
H-2 and H-9 were placed into a 4J relationship,
whereas protons H-2 and H-10 were placed into a 3J relationship. A 7.2 Hz 3J coupling
and an unobservable 4J coupling may have
seemed more reasonable by the authors of the original assignment but
are fully explained by the revised structure.Proton H-9 is
located at one of the one-carbon bridges of the bicyclo[2.1.1]hexane
core of 1b. The chemical shift of its signal around δ
2.9230 ppm is at the higher end of what is expected for a methine
hydrogen on a carbon adjacent to a ketone. Curiously, this signal
appears to be a singlet even though it has 3J relationships with H-2 and H-10, both of which are also on the cyclobutane
ring. The unobservable (calculated at 0.074 Hz) 3JH-9,H-10 coupling constant must
be attributed again to a nearly 90° dihedral angle. In the original
aquatolide structure, proton H-9 was also placed at a three bond distance
from H-10, but no explanation was offered for the existence of the
small coupling constant.H-10 is on the opposite bridgehead
carbon from H-2 of the bicyclo[2.1.1]hexane
core. It is reported as a dd resonance at δ 2.6411 ppm in both
the original publication and the revision article.
Resolving
Overlapped Aquatolide “Multiplets”
The resonances
of the four hydrogens of the two contiguous methylene
groups are crowded into the δ 1.84–2.54 ppm interval.
Their complex splitting as well as the possible dynamic nature of
the ring at these positions tends to obscure the multiplicities and
determination of coupling constants. The present study assigns the
relative positions of 4a, 4b, 5a, and 5b based on Karplus relationships
and unambiguously assigned chemical shift values and reconfirms the
assignments through the previously reported NOEs.H-4a exhibits
the most downfield chemical shift of the four methylene hydrogens
and has previously been designated as a dd. H-4a is geminally coupled
to H-4b with a magnitude of −16.172 Hz. H-4a has a reported
6.7 Hz coupling constant with its 3J H-5b
neighbor. On the other hand, the 3JH-4a,H-5a coupling is small and not easily observable;
optimized processing revealed the underlying complexity of the signal
and allowed determination of 3JH-4a,H-5a as 2.794 Hz. Chemical shifts and coupling patterns are consistent
with the position of H-4a pointing into the eight-membered ring in
close proximity to the ketoneoxygen and H-10. At this position, the
dihedral angle between H-4a and H-5a is nearly 90°, and the dihedral
angle between H-4a and H-5b approaches 135° with 3JH-4a,H-5b being observed
as 6.766 Hz. The position of H-4a is confirmed with NOESY, which shows
correlations to both H-10 and H-4b. The resonance is a broad ddd due
to an underlying 0.298 Hz 4JH-4a,H-6 coupling.The signal for H-4b has the most upfield chemical
shift of the
four methylene hydrogens and is centered at δ 1.9657 ppm. This
proton was previously designated as a multiplet. In addition to the 2JH-4a,H-4b coupling
of −16.172 Hz, H-4b shows 3J couplings
with H-5a and H-5b, which are easily obscured in this complex signal.
The small 1.578 Hz coupling may be attributed to 3JH-4b,H-5a, whereas the large 3JH-4b,H-5b coupling
was determined as 11.763 Hz.Proton H-5a signal resonates between
H-4a and H-5b and has also
previously been designated as a multiplet. Upon closer examination,
however, this signal appears as a very complex but clearly defined
ddddq, as seen in Figure . There is a possible total of 64 individual peaks, but overlap
considerations bring it down to 36 discernible lines. The reason that
this signal exhibits sharper lines than H-5b, H-4a, and H-4b may be
related to the fact that the C-5 to H-5a σ bond is aligned with
the neighboring sp2 orbitals at C-6. The sp3 hybridized orbitals of H-5a and the C-5 bond are aligned or nearly
aligned with the π orbitals of the C-6 to C-7 double bond, imparting
the orientation of the C–H bond. Possible dynamic movement
of the C-5–C-6–C-7 carbon array, which produces four
major conformations (see pages S36 ff. of ref (2)), lead to a specific (T, B, c) and characteristic time-averaged spin coupling pattern,
especially for the protons at C-5. This portion of the aquatolide
molecule is the only substructural fragment that is likely to give
rise to dynamic movement, the rest of the molecule being fairly rigid.
However, because of the allylic orientational effect, a slight barrier
may exist, thus favoring only one of the conformations with aquatolide
then being rendered semirigid. A study involving a structural arrangement
similar to the present case (6- vs 8-membered ring in aquatolide)
was observed for 3-aryl-5r-aryl-6t-carbethoxycyclohex-2-enones.[23] The largest coupling constant is attributed
to a geminal JH-5a,H-5b coupling
(−20.006 Hz), which separates the signal into two almost baseline
separated subpatterns. The 3JH-5a,H-4a and 3JH-5a,H-4b couplings have already been described. Protons H-4b, 5a, and 6 appear
to orient themselves toward the outside of the 8-membered ring (Figure ). A 3.208 Hz 3JH-5a,H-6 coupling
is also observed, and the observed quartet may be attributed to a
2.142 Hz homoallylic 5JH-5a,H-13 coupling. Homoallylic couplings have been described by Jackman and
Sternhell for a number of cases.[24] An example
that resembles aquatolide exhibits a 1.8 Hz homoallylic coupling reported
in a 6-methyl-3,4-dihydro-2H-pyran.[25]
Figure 5
Optimizing
processing parameters reveal coupling constants and
line counts present in the signals for H-5a and H-6 of 1b. Double zero filling was applied to both. The bottom (blue) signals
were obtained using a Lorentzian–Gaussian apodization function
of LB = −1.4 Hz and GF = 0.17 (17% AQ). The top (black) signals
resulted from a Lorentzian–Gaussian apodization function of
LB = −2.5 Hz and GF = 0.25 (25% AQ) and demonstrate that all
theoretical lines of these complex “multiplets” can
indeed be deciphered by manual analysis facilitated by tools such
as jVisualizer (http://jvisualizer.sourceforge.net/). Actually,
proton H-5a resonates as a ddddq, and H-6 gives rise to a ddq signal.
Figure 6
Three-dimensional representation of 1b showing the
spatial relationships in the 8-membered ring computed with density
functional theory.[2]
Upon closer examination, the H-5b “multiplet” located
between the H-5a and H-4b signals is identified as a ddddq. The 3JH-5b,H-6 coupling
may be observed as 4.769 Hz. The homoallylic 5JH-5b,H-13 coupling exhibits a similar J coupling value (2.245 Hz) to that of 3JH-5a,H-13.
Protons of
the Olefinic Moiety
The signal for the olefinic
proton at H-6 has a chemical shift of δ 5.8507 ppm. It was reported
as a multiplet in the original publication and as a ddt in the revision
article. The 3JH-5a,H-6 and 3JH-5b,H-6 couplings described above are in agreement with previous work on
allylic couplings.[2] Therefore, the multiplicity
of the signal should be accurately represented as a ddq (Figure ). There are a total
of 16 peaks in this signal: ten are readily discernible and six require
stronger Lorentzian–Gaussian resolution enhancement to be discernible.Optimizing
processing parameters reveal coupling constants and
line counts present in the signals for H-5a and H-6 of 1b. Double zero filling was applied to both. The bottom (blue) signals
were obtained using a Lorentzian–Gaussian apodization function
of LB = −1.4 Hz and GF = 0.17 (17% AQ). The top (black) signals
resulted from a Lorentzian–Gaussian apodization function of
LB = −2.5 Hz and GF = 0.25 (25% AQ) and demonstrate that all
theoretical lines of these complex “multiplets” can
indeed be deciphered by manual analysis facilitated by tools such
as jVisualizer (http://jvisualizer.sourceforge.net/). Actually,
proton H-5a resonates as a ddddq, and H-6 gives rise to a ddq signal.Three-dimensional representation of 1b showing the
spatial relationships in the 8-membered ring computed with density
functional theory.[2]The olefinic methyl group, H-13, with a signal centered at
1.8698
ppm, was reported as a multiplet in the original publication and as
a quartet in the revision article. As the H-13 protons are coupled
to H-5a, H-5b, and H-6, with J couplings of 2.142,
2.245, and 1.546 Hz, respectively, it should be described as a ddd.Both methyl groups on the gem dimethyl moiety are reported as singlets
in the original publication and in the revision article. The methyl
group that is closest to the lactone (Figure ) is designated as C-14, whose hydrogens
have a 1H chemical shift of δ 1.0544 ppm. The methyl
group that is closest to H-9 is designated as C-15 with hydrogens
at δ 1.1941 ppm. This orientation is revealed in the NOESY spectrum,
which shows the protons at δ 1.1941 ppm correlated strongly
with H-9 and more moderately with H-1, H-10, and H-14.
Visualizing
2D NMR Data with QuILTS: NOE Correlations
The QuILT concept,
introduced above for 1D HNMR, can be employed
to represent the entirety of a complex 2D NMR cross-peak map into
a more straightforward graphical format. In the case of aquatolide,
the NOESY correlations are essential to confirm and/or determine key
structural elements. As shown in the corresponding correlation map
(original NOESY QuILT, Figure A), plotting internuclear distances on the upper diagonal
relative to cross peaks on the lower diagonal, the NOESY approach
may be a hit-or-miss situation. Expected NOESY correlations may or
may not be observed with a given set of acquisition and processing
parameters. Of particular concern with the structure determination
of aquatolide in the original article is the apparent lack of correlations
for the crucial H-1, H-2, H-9, and H-10 protons, such as H-2 to H-10
(Figure A). Without
these correlations, it is difficult to confirm the original structure.
The revision article described a much more complete family of NOESY
correlations (revised NOESY QuILT, Figure B), especially between the four key protons
of the bicyclo[2.1.1]hexane core, such a H-2 to H-9. However, there
are still some areas left for consideration. An apparent cross peak
between H-2 and H-10 seems to favor the original structure over the
revised structure. This is likely due to the presence of an antiphase
cross peak, or COSY cross peak, resulting from a coherence transfer
between J-coupled spins.[26]
Figure 7
NOESY
correlation maps (NOESY QuILTs) of the original (A) and the
revised (B) structures (δ precision as reported). The upper
right halves contain the distances between nuclei taken from the revision
article and a 3D model (in parentheses). Red color indicates distances
<3.0 Å. Yellow boxes are distances between 3.0 and 5.0 Å.
Boxes without color represent distances >5.0 Å. The bottom
left
halves are actual NOESY cross peaks observed as either strong (xx)
or weak (x) correlations. Distances without parentheses were taken
from the revision article, and those in parentheses were determined
with Avogadro molecule editor and visualizer.
NOESY
correlation maps (NOESY QuILTs) of the original (A) and the
revised (B) structures (δ precision as reported). The upper
right halves contain the distances between nuclei taken from the revision
article and a 3D model (in parentheses). Red color indicates distances
<3.0 Å. Yellow boxes are distances between 3.0 and 5.0 Å.
Boxes without color represent distances >5.0 Å. The bottom
left
halves are actual NOESY cross peaks observed as either strong (xx)
or weak (x) correlations. Distances without parentheses were taken
from the revision article, and those in parentheses were determined
with Avogadro molecule editor and visualizer.A detailed analysis of the revised NOESY QuILT (Figure B) shows that H-1
correlates
with H-2, H-9, H-14, and H-15. H-2 correlates strongly with both H-1
and H-9 while being more moderately correlated with H-5b, H-6, H-10,
H-14, and H-15. The NOESY spectrum of H-9 shows a strong correlation
to the H-2 and H-15 methyl protons and weaker correlations to H-1,
H-13, and H-10. H-10 shows correlations to H-2, H-4a, H-4b, H-9, H-14,
and H-15. The position of H-4a relative to H-4b is also supported
by the NOESY spectrum as H-4a correlates to H-4b, H-5a, H-5b, and
H-10. In turn, H-4b is correlated to H-4a, H-5a, and H-10. H-5a shows
NOE contacts to H-4a, H-4b, H-5b, and H-6. The position of H-5b relative
to H-5a is supported by NOESY correlations to H-2, H-4a, H-5a, and
H-6. The latter shows a correlation with the H-13 methyl protons,
which in turn exhibit a correlation with H-6 and H-9. As previously
described, the relative orientation of the C-14 and C-15 methyl groups
relies on the NOESY data.
QuILT Representation of the 2D NMR Workhorse
HMBC
The
HMBC experiment is a powerful method to confirm or predict structural
connectivity features via long-range heteronuclear coupling (≥2JC,H). Heteronuclear correlations
play an important role in the overall structural determination, but
there are some important limitations. A survey of marine natural product
revisions suggested that a significant number of misassigned structures
are associated with interpretation of the HMBC data.[27] This was primarily due to the incomplete nature of the
experimentally observed HMBC correlations. This situation can be clearly
seen, in the case of aquatolide, with the HMBC QuILT shown in Figure , which by nature
is asymmetric. In the original publication, 9 of 24 2JC,H and 19 of 42 3JC,H possible correlations were observed. In the revision
publication, 13 of 24 2JC,H and 37 of 45 3JC,H possible
correlations were observed. From these examples, it may be proposed
that, at best, HMBC data may be used to favor one set of possible
structures rather than actually proving one structure.
Figure 8
Long-range heteronuclear QuILTs summarize both the observed
direct
(1JC,H) and ≥2JC,H correlations in the original (A; HETCOR and long-range HETCOR, respectively) vs revised
(B; HSQC and HMBC, respectively) aquatolide structures.
The numbers inside the δ and atom number grid reflect the number,
n, of connecting bonds (nJ). Bolded numbers
represent observed correlations. Color coding of boxes: black = one
bond, violet = two bonds, blue = three bonds; white = four and more
bonds. Color coding of numbers: black and white = 1JC,H correlation; gray ≥2JC,H correlations.
Similar
to all NMR techniques, both the acquisition and processing parameters
play a substantial role in what correlations may be observed or not
observed. For example, the absence of key 3J HMBC correlations, which will exhibit variation according to the
3-bond Karplus relationship between the 1H and 13C, may be a result of the experimentally acquired data falling outside
of the coupling constant range in the standard HMBC experiment, which
is typically optimized for 3JC,H = 7.0–8.5 Hz for 1H, 13C dihedral angles
of 180°. It is frequently necessary to perform two or three HMBC
experiments optimized for smaller J-couplings (3JC,H = 4.0–6.0 Hz) and/or
extend the number of increments of the evolution time to reveal the
smaller couplings that occur later in the evolution time. To reveal
the maximum number of correlations, other experiments may be used
for extracting couplings over 3–5 bonds, e.g., LR-HSQMBC.[28] Heteronuclear correlation experiments do not
typically reveal if an observed cross peak represents a 2-, 3-, or
even 4-bond coupling. Fully and correctly assigning all protons and,
thus, all protonated carbons would serve to reduce this ambiguity
considerably.Long-range heteronuclear QuILTs summarize both the observed
direct
(1JC,H) and ≥2JC,H correlations in the original (A; HETCOR and long-range HETCOR, respectively) vs revised
(B; HSQC and HMBC, respectively) aquatolide structures.
The numbers inside the δ and atom number grid reflect the number,
n, of connecting bonds (nJ). Bolded numbers
represent observed correlations. Color coding of boxes: black = one
bond, violet = two bonds, blue = three bonds; white = four and more
bonds. Color coding of numbers: black and white = 1JC,H correlation; gray ≥2JC,H correlations.The heteronuclear QuILTs from the original aquatolide publication
data (Figure A) shows
that all of the observable cross peaks in the long-range HETCOR experiment
may be attributed to 2JC,H and 3JC,H correlations. Although this
was congruent with the original structure, the incompleteness of the
correlation map (a well-known downside of the long-range variant of
the HETCOR experiment[29]) was consistent
with other possible structures as well. An HMBC 2D experiment in the
revision article identified several key relationships (HMBC QuILT, Figure B), but this set
alone could not definitively favor the revised structure over the
original one and required additional evidence. Notably, there are
seven instances where a JC,H coupling
is 3JC,H for the revised structure
and would be 4JC,H for the
original. The five correlations that are identifiable as cross peaks
in HMBC are C-1 to H-9, C-4 to H-10, C-8 to H-2, C-10 to H-4a, and
C-10 to H-4b. However, two 3JC,H couplings are not evident: C-9 to H-1 and C-12 to H-10. Conversely,
there are five instances where observed JC,H couplings are 4JC,H for the
revised structure that would be 3JC,H for the original structure. Accordingly, in line with the
revision, four of them are not seen as HMBC cross peaks (C-4 to H-9,
C-5 to H-13, C-9 to H-4a, and C-9 to H-4b), whereas one is indeed
observed: C-12 to H-9. Although these provide a strong argument for
the revised structure over the original, these results are not overwhelmingly
conclusive. In particular, the only 4JC,H coupling observed for the revised structure must be
addressed. The geometry of the correlating moiety has a characteristic
“W” arrangement that would allow the back lobes of sp3 orbitals on C-3 and C-9 to overlap, thus providing a mechanism
for the transmission of the observed spin coupling effects.
HiFSA
of Synthetic Aquatolide Provides Independent Confirmation
While this manuscript was under preparation, the group of HH published
the total synthesis of aquatolide.[30] Sharing
of the 400 MHz 1H NMR spectrum FID of this publication
and a 1.1 mg sample of the compound, which was used to acquire a 900
MHz data set, permitted both a rapid verification of the result of
this work and the mutual congruence of the structural assignments.
For this purpose, the HiFSA profiles of the 400 and 900 MHz data of
the synthetic sample were generated and compared with the profile
obtained from the 800 MHz of the natural material. The results (Table ) reveal the expected
high consistency of all three profiles and also confirm the reported
scaling capability of HiFSA.[9] Furthermore,
in line with the interpretation of the dynamic effects that broaden
the signals of H-4a, H-4b, and H-5a of the 8-membered ring (see above),
the small but significant differences observed for the couplings of
these protons reflect the impact of the magnetic field strength on
the peak separation, leading to greater line broadening due to incomplete
averaging as well as the slight experimental differences of the two
measurements (temperature and concentration). Accordingly, the minor
deviations in the J-patterns actually confirm the
inferences regarding the peak broadening effects.
Table 1
Comparison
of the HiFSA Profiles of
Natural (1b-800 = 800 MHz Data from ref (2)) vs Synthetic Aquatolide
(1b-400 = 400 MHz from ref (30) and 1b-900 = 900 MHz of Sample
Originating from ref (30)) Shows the Close Congruence of the Spin Systems in the Coupling
Constants (A), Chemical Shifts (B), and Line Widths of the Resonances
(C), Confirming the Identity of the Samplesa
A
J (Hz)
1b-800
1b-400
1b-900
H10A–H14B
–0.25
–0.62
–0.20
H10A–H15B
–0.13
–0.51
–0.12
H10A–H1A
1.85
1.90
1.82
H10A–H2A
7.22
7.21
7.22
H10A–H9A
0.24
0.00
0.15
H13B–H5A
2.22
2.13
2.19
H13B–H5B
2.17
2.11
2.16
H13B–H6A
–1.56
1.59
1.55
H1A–H2A
2.50
2.48
2.50
H1A–H9A
–0.39
–0.08
–0.40
H2A–H4A
–0.35
–0.04
–0.41
H2A–H4B
–0.26
–0.03
–0.22
H2A–H9A
0.45
0.50
0.37
H4A–H4B
–16.20
–16.20
–16.20
H4A–H5A
3.03
1.92
2.48
H4A–H5B
6.77
6.81
6.80
H4A–H6A
0.96
0.95
1.00
H4B–H5A
11.7
12.1
12.3
H4B–H5B
1.60
1.60
1.62
H4B–H6A
–0.09
0.00
–0.34
H5A–H5B
–20.00
–19.90
–20.00
H5A–H6A
3.26
3.19
3.25
H5B–H6A
4.76
4.64
4.72
The small but diagnostic differences
in the J values and increased signal widths of H-4A,
H-4B, and H-5B reflect the field-dependent dynamic of the 8-membered
ring system (see main text).
Overall, we
learn from this comparison that dynamic effects play enough of a role
in HiFSA profiles such that they have subtle but characteristic effects
on the determined coupling constants in complex signals. When interpreting
these subtle effects, one has to keep in mind that the observed coupling
constants represent weighted averages of the coupling constants of
all conformers. Therefore, dynamic effects influence coupling constants
as determined by HiFSA and include temperature, field strength, and
sample concentration. Furthermore, line distances in 1H
NMR spectra are not coupling constants, unless the spin system is
pure first order, which is rarely truly the case and is certainly
not the case in aquatolide. Representing an iterative method, HiFSA
determines the “experimental” coupling constants, but
the underlying NMR experiment, detects conformationally averaged coupling
on the (slow) NMR time scale. As a result, unless all populations
and their abundance are known, the “true” underlying J values cannot be determined.The small but diagnostic differences
in the J values and increased signal widths of H-4A,
H-4B, and H-5B reflect the field-dependent dynamic of the 8-membered
ring system (see main text).
Conclusions
Understanding the reasons for misassignment
is as important as
correcting structures. The following points summarize key lessons
to be learned, or reminded of, from the aquatolide case.
Point 1: 1D 1H NMR Data is Indispensable
The proper acquisition
and accurate interpretation of 1D1H data (the “mother
of all NMR spectra”) is a crucial
first step in structure elucidation. Especially for the purpose of
obtaining preliminary structural information, 1H spectra
will usually be the first 1D spectra acquired, and this choice is
largely driven by sensitivity, due to the limited levels of material
frequently encountered early in an isolation protocol. Subsequent
1D and 2D experiments will expand on and/or confirm the 1D1H data. Although the 1D13C data is particularly important
to elucidate proton-deficient molecules, NMR spectra of both nuclei
are important for subsequent structural dereplication. The importance
of 1D1H data should be respected, beginning with acquisition
of the data, and followed through with the appropriate post-acquisition
processing. In particular, Lorentzian–Gaussian or other resolution
enhancement post-acquisition processing, including zero-filling, can
be used to observe the greater details of coupling patterns present
in complex signals. However, it must be conceded that even meticulous
processing may not reveal all of the signal information and, therefore,
coupling information due to signal overlap, exceedingly small coupling
values, and signal-to-noise issues, may still make extraction of all
of the spectral information problematic.In this context, it
should be noted that standard 1H NMR spectra acquired under
quantitative conditions are entirely fit for the purpose of qHNMR
quantitation, allowing for the assessment of the purity of the investigated
compounds. As qHNMR spectra need to be acquired with good signal-to-noise
(S/N), they elegantly serve the dual purpose[10] of enabling recognition of splitting/coupling patterns through resolution-enhanced
post-acquisition processing and LC-independent purity assessment as
required by journals.[10]
Point 2: Protons
and Carbons are Indicators of Backbone Geometry
Computational
evaluation of structures using both 1H
and 13C data, together with the calculation of Δδ
values, is the first tier in the evaluation of a proposed structure.
Prediction of coupling constants based on the optimized geometry of
the proposed structure is the second tier of 1H spectra
evaluation. Finally, the observed coupling information may be further
enhanced with iterative fitting processes utilizing the quantum mechanical
spin information inherent in the structural geometry in a third tier
of evaluation. Although HiFSA may ultimately reveal inconsistencies
in a proposed structure, a careful analysis of the HiFSA parameters
must still be undertaken even in the case of a good fit.Primarily,
the evaluated 3J coupling constants should
be consistent with the dihedral angles present in the proposed 3D
molecular structure. Of particular concern are instances of unobservable 3J coupling constants due to dihedral angles
near 90°: the lack of measurable coupling differs significantly
from missing J values in reported tables or QuILTs.
Therefore, it is a necessary requirement to verify both what is observed
and what is not observed. It is difficult to know from the literature
how often unobservable 3J couplings occur
in structural elucidation: as “unobservables”, they
cannot be observed and thus are not reported, but so are many other
obvious couplings.Whereas the computation of average and maximum 13C chemical
shift deviations is an accepted means of assessing the plausibility
of (revised) structures,[31] the accuracy
of available 1H chemical shift prediction tools is not
yet sufficient to establish analogue measures for 1H-based
computer-aided structure elucidation (CASE; http://www.acdlabs.com/comm/elucidation/2013_10.php). However, precise and accurate reporting of 1H NMR data
(see ref (16) and below)
is an important and powerful instrument of both dereplication and
structure elucidation.
Point 3: 1D 1H NMR Data is Information-Rich
The simplicity of the 1D1H NMR experiment has a tendency
to hide the information richness of the spectra. In fact, with the
exception of proton-deficient compounds, the assortment of multibond
couplings (2–7J) that encodes the
network of proton resonances of a given molecule provides plentiful
structural information, and all of them have to be compatible with
the proposed structure. A generally useful approach is to challenge
“multiplets” as particularly information-rich signals.
One efficient means of mining this information is to perform full
spin analysis (HiFSA), which captures the 1H spin network
assignments in a QM-proof manner. Spin simulation software, required
for this purpose, has been available since the 1960s (LAOCOON), and
modern tools are more powerful than ever. It is important to note
that the assignment of all chemical shifts and couplings requires
spectral simulation to account for non-first-order effects, which
are frequently observed even with “simple” molecules
and at high magnetic field strengths.Part of the realization
of the information richness is the consideration of long-range couplings
as both a subtlety to be explored and a great resource for structural
information. The occurrence of long-range couplings indicates particular
and sometimes unique structural characteristics. For example, in the
aquatolide case, allylic 4J, homoallylic 5J, and strained ring 4J “twofold W” couplings were observed. Although
long-range couplings might be viewed as minor and “esoteric”,
they can impart important and valuable constraints as to the plausibility
of a particular structure.
Point 4: 2D NMR Supports but does not Replace
1D NMR
Because of the general accessibility of 2D data, 1D
NMR experiments
have taken a “backseat” in the structure elucidation
toolbox. However, it is important to realize that one cannot rely
solely on the workhorse 2D NMR spectra (COSY, HSQC, HMBC). The evidence
contained in 1D data sets, particularly in the 1H domain
involving abundant J coupling, simply cannot be ignored
when making conclusions about the structure; all of the data, including
the 1D1H information, has to match. Collectively, 2D NMR
experiments can serve to confirm structural assignments, including
those made from 1D1H analyses, but not replace or even “override”
them as evidence. Another important reflection resulting from the
aquatolide case: although the lack of an HMBC (or any other 2D) cross-peak
can be diagnostic, it is predominantly a lack of information. It can
be due to either structural constraints or be an artifact of the acquisition
parameters. The observation of an unexpected strong HMBC cross-peak
is a clear warning sign of a wrong structure. In fact, peak intensities
and JC,H coupling values play an important
role in the correct interpretation of HMBC and other 2D NMR experiments
that involve J coupling mechanisms.
Point 5: FID Archives
Proper preservation and dissemination
of experimental FIDs in electronic format is an important aspect of
any structural elucidation process. This conforms to the principle
of the dissemination of scientific research results. Adequate information
must be supplied in order that research results may be reproduced.
The availability of FIDs permits a comparison of the NMR data for
published structures with NMR data for newly acquired compounds either
by isolation or by synthesis for facilitating dereplication and identifying
novel structures.Dereplication based solely on typically published 1H chemical shift and multiplicity tables is insufficient.
Even if high resolution spectra (images) are included in the Supporting
Information of a publication, the opportunity for accurate dereplication
cannot be achieved. Therefore, the original FIDs in electronic format
should be supplied as part of the dissemination of published work.
Point 6: Free Databases
The compilation and maintenance
of databases, such as the crystallography open database,[32] is a worthwhile contribution to the field of
structure elucidation. Fledgling NMR FID databases have emerged,[33,34] but a concerted effort by both journal editors and publication authors
to participate is overdue. One unresolved but important aspect is
the status of the distributed information. Most desirable for scientific
purposes are Free Archives which, similar to Free Software, are not
just freely accessed, but also associated with distribution rights
that establish the freedom to use the data portion of an ongoing evolutionary
process and methodology improvement with reference to the original
authors.
Point 7: Dereplication Requires Reproducibility of Chemistry
as a Central Science
The consistency of structure elucidation
reports and their efficient dissemination has broad implications not
only for accurate publication of chemical structures but also for
exploitation of these structures for their biological, pharmaceutical,
and environmental applications. In the current situation, as described
in the Introduction, much research has been
expended for the synthesis of molecules exhibiting interesting biological
activities, only to find that the structures originally reported were
incorrect.[8,35] The reproducibility of new structures and
related discoveries rests on the ability of future researchers to
dereplicate the structure and possibly reassess the sample, or at
least its 1H NMR spectrum. The HiFSA-based dereplication
of synthetic relative to isolated aquatolide presented in the section
“HiFSA of Synthetic Aquatolide”
exemplifies the efficiency of the approach.Dereplication and
reproducibility are two sides of the same coin. Near-identical (but
not really identical!) chemical properties are the breeding ground
for wrong assignments, misidentification, synthetic chemistry misdirection,
and wasted time and resources, leading to long-lasting confusion in
upstream and downstream research. Concerning 1H NMR, subtleties
drive dereplication. In fact, attention to detail can turn standard
1D1H NMR into a powerful dereplication tool. This applies
particularly to natural products, as their combinatorial, biosynthetic
origin makes the existence of very close or near-identical congeners
with partial stereochemical variations very likely. At the same time,
1D13C NMR represents a complementary approach to dereplication
that is readily automated due to the simplistic pure shift nature
of 1H broad-band decoupled 13C spectra.There are numerous cases of natural products that represent near-identical
molecules, which are highly likely to produce near-identical NMR spectra
(e.g., the [iso-]silybins),[13] but are also
likely associated with distinct biological properties and/or taxonomic
sources, and sometimes new chemical structures (e.g., leubethanol
from the plant Leucophyllum frutescens vs elisabethanol
from the gorgonian octacoral Pseudopterogorgia elisabethae).[36] Even when congeneric molecules are
not near-identical themselves, but only with regard to their (highly
similar) 1H NMR spectra, the comprehensive 1H NMR analysis is well-suited to produce compelling structural evidence
as well as highly specific data for structural dereplication and reproducibility
(see below). One example of a new chemical structure investigated
using this approach is the new antituberculosis drug lead ecumicin.[37] Finally, it is important to point out that chemical
shifts exhibit solvent dependence; therefore, this is another significant
consideration in NMR-based dereplication.
Best Practices Enhance
Reproducibility
From a conceptual
perspective, successful dereplication requires unideterminant structural
parameters. HiFSA profiles can be considered as one unideterminant
data set for a given structure and provides a potential substitute
for the mixed melting point determination representing the gold standard
for chemical identity, especially if the second cannot be determined
due to practical/sample limitations. Consequently, the following tenets
are simple ways to enhance reproducibility by means of best practices
in NMR-based structural analysis: (i) assign all protons (and carbons)
and all couplings; (ii) report chemical shifts (δ) precisely
to three or even better four decimal places (≤1 ppb); (iii)
report coupling constants (J) precisely to one or
even better two decimals (≤100 mHz); (iv) perform full spin
analysis (e.g., HiFSA) and report complete sets of 1H spin
parameters, e.g., as supporting text or vendor-specific but open formats,
such as PERCH PMS files; and (v) make raw NMR data (FIDs) publically
accessible and part of publications.Certainly, there are additional
best practices related to the acquisition of 1H NMR spectra,
which will in turn enhance the reliability and reproducibility of
interpretation. These best practices include (i) the habit of depleting
dissolved oxygen in the sample (freeze–pump–thaw or
He degassing) and (ii) being cognizant of how solvents affect the
acquisition and characteristics of 1H NMR spectra. For
example, the chloroformdeuterium signal may be difficult to lock
at high fields;[38] thus, solvent effects
on line shape (viscosity) and shimming (split fields) should also
be considered.
Documentation and Completeness of Structural
Evidence
The QuILTs introduced herein are highly comprehensive
representations
of NMR structural evidence. The QuILT format is more intuitive for
human use than the ubiquitous tabular or graphical formats used in
the laboratory and in publications today. In particular, QuILTs simplify
the assessment of the completeness of the NMR structural information,
as empty boxes are spotted readily and represent the only allowed
gaps, indicating a lack of correlation that is in line with the proposed
structure.Moreover, QuILTs are flexible in accommodating the
most common NMR experiments: 1D1H (1H J-QuILT in Figure ), homonuclear (e.g., NOESY QuILT in Figure ; can be expanded to, e.g., TOCSY), and heteronuclear
(e.g., HMBC QuILT in Figure ; can be expanded to HSQC as diagonal) spectra can all be
transposed in the QuILT format.Finally, the QuILT format can
be readily standardized and provide
NMR data in a machine readable, unified format, making it an ideal
reporting format for computational processing. Potential downstream
applications of data published in QuILT format include, but are not
limited to, spectroscopic databases, dereplication, and computer-assisted
structure elucidation tools.
Limitations of Evidence
in Structure Elucidation
Collectively,
all above points reflect on the generally well-known but sometimes
forgotten fact that spectroscopic structure elucidation is based on
indirect rather than direct evidence and is the product of deductive
reasoning rather than a “picture” of the molecule. As
a result, spectroscopic evidence is intrinsically limited, and respecting
this limitation is key to sound structure elucidation. The imperative
of always considering alternative structures is one valuable means
of addressing this challenge. Another is to distinguish the difference
between the terms “proof” and “consistent with”
in structure elucidation documents. The case of aquatolide exemplifies
some of the pitfalls, but also new insights, that can be gained from
adhering to these principles as closely as possible.
Experimental Section
NMR Spectroscopy
The NMR measurements were described
previously for the natural aquatolide (800 MHz)[2] and the synthetic material (400 MHz).[30] A sample of unnatural (−)-aquatolide (1.1 mg in
0.7 mL CDCl3) was also subject to 900 MHz NMR analysis.
For reprocessing of the 1H FID, the chemical shift of the
residual solvent signals, CHCl3, at δH 7.2600 was used as the chemical shift reference. The 800 MHz data
for Figure A and Figure A were processed
using Lorentzian–Gaussian apodization functions with LB values
of −1.0 to −3.0 Hz and Gaussian factors of 0.10–0.30,
centering the Gaussian function at 10–30% of the acquisition
time. For HiFSA, reprocessing using a mild Lorentzian–Gaussian
window function (line broadening = −0.3, Gaussian factor =
0.05) prior to two zero fills to 256 K and Fourier transformation.
Computer-Aided NMR Spectral Analysis
The 1H iterative
full spin analysis (HiFSA) was performed by PERCH NMR
software package (ver. 2013.1) as described previously.[9,39] The optimized spectral parameters were saved as PERCH parameter
text files (*.pms). Four and two decimal places for δH and J values, respectively, were considered significant.
The measurements of interatomic distances were performed with the
free software Avogadro (http://avogadro.openmolecules.net) v1.1.1[40] using the MOL files exported
by PERCH.
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