Journal of Natural Products
Article
compound 2, since experimental data revealed that it differs from 1
only by the presence of a β-D-glucopyranosyl unit. Optimization of the
3D structures was performed with MacroModel 10.239 using the OPLS
force field40 and the Polak−Ribier conjugate gradient algorithm
(PRCG, maximum derivative less than 0.001 kcal/mol).
In particular, for compound 1, which has three stereogenic centers
and an axis of chirality, eight possible diasteroisomers were considered:
1a (aR*,8S*,9R*,10R*), 1b (aS*,8S*,9R*,10R*), 1c
( a R * , 8 S * , 9 R * , 1 0 S * ) , 1 d ( a S * , 8 S * , 9 R * , 1 0 S * ) , 1 e
(aR*,8S*,9S*,10R*), 1f (aS*,8S*,9S*,10R*), 1g (aR*,8S*,9S*,10S*),
For compound 3, possessing four stereogenic centers and an axis of
chirality, 16 diastereoisomers were considered: 3a
(aR*,8S*,9R*,10R*,11R*), 3b (aS*,8S*,9R*,10R*,11R*), 3c
(aR*,8S*,9R*,10R*,11S*), 3d (aS*,8S*,9R*,10R*,11S*), 3e
(aR*,8S*,9R*,10S*,11R*), 3f (aS*,8S*,9R*,10S*,11R*), 3g
(aR*,8S*,9R*,10S*,11S*), 3h (aS*,8S*,9R*,10S*,11S*), 3i
(aR*,8S*,9S*,10R*,11R*), 3j (aS*,8S*,9S*,10R*,11R*), 3k
(aR*,8S*,9S*,10R*,11S*), 3l (aS*,8S*,9S*,10R*,11S*), 3m
(aR*,8S*,9S*,10S*,11R*), 3n (aS*,8S*,9S*,10S*,11R*), 3o
(aR*,8S*,9S*,10S*,11S*), 3p (aS*,8S*,9S*,10S*,11S*) (Chart S2,
(8S*,9R*,10R*)-1 and the transition state confirmed the hindered
rotation about the biphenyl axis (Results and Discussion). The
different atropisomers could be differently treated for the subsequent
calculations of the NMR parameters and for the computation of the
CD spectra.
Following the same procedure, the energy of the transition state
associated with the interconversion between (aR) and (aS)
atropisomers of 4′ (4′a and 4′b, respectively; Chart 3, Supporting
The computation of the 13C and 1H NMR chemical shifts was
performed on all the selected conformers for the different
diastereoisomers of compounds 1 and 3, using the MPW1PW91
functional, the 6-31+G(d,p) basis set, and MeOH IEFPCM. Final 13C
and 1H NMR spectra for each of the diastereoisomers were built
considering the influence of each conformer on the total Boltzmann
distribution taking into account the relative energies. Calibrations of
1
calculated 13C and H chemical shifts were performed following the
multistandard approach.24,25 In particular, sp2 13C and 1H NMR
chemical shifts were computed using benzene as reference
compound,24,25 while TMS was used for computing sp3 13C and H
1
chemical shift data.
A further set of data was produced using only TMS as reference
compound, and it was subsequently used for the computation of the
DP4+ probabilities.
Furthermore, for compound 4′, possessing an axis of chirality, two
atropisomeric forms, 4′a (aR) and 4′b (aS), are reported in Chart S3,
First, experimental and calculated 13C and 1H NMR chemical shifts
were compared computing the Δδ parameter (Tables S1−S8,
Starting from the obtained 3D structures, exhaustive conformational
searches at the empirical molecular mechanics level with the MCMM
method (50 000 steps) and LMCS method (50 000 steps) were
performed, in order to allow a full exploration of the conformational
space. Furthermore, molecular dynamics simulations were performed
at 450, 600, 700, and 750 K, with a time step of 2.0 fs, an equilibration
time of 0.1 ns, and a simulation time of 10 ns. A constant dielectric
term of methanol, mimicking the presence of the solvent, was used in
the calculations to reduce artifacts.
Δδ = |δexp − δ
|
calc
where δexp (ppm) and δcalc (ppm) are the 13C/1H experimental and
calculated chemical shifts, respectively.
The mean absolute errors for all the considered diastereoisomers
were computed using the following equation:
For each diastereoisomer, all the conformers obtained from the
conformational searches were minimized (PRCG, maximum derivative
less than 0.001 kcal/mol) and compared. The “Redundant Conformer
Elimination” module of Macromodel 10.239 was used to select
nonredundant conformers, excluding those differing by more than 21.0
kJ/mol (5.02 kcal/mol) from the most energetically favored
conformation and setting a 0.5 Å RMSD (root-mean-square deviation)
minimum cutoff for saving structures. For compounds 1, 3, and 4′,
MM conformational searches produced both sets of atropisomers,
which were manually separated after visual inspection once the
hindered rotation along the biaryl axis was assessed by means of
quantum mechanical calculations (vide infra). All the QM calculations
were performed using Gaussian 09 software.41
∑ (Δδ)
MAE =
n
defined as the summation (∑) of the n computed absolute error
values (Δδ), normalized to the number of chemical shifts considered
Furthermore, DP4+ probabilities related to all the stereoisomers of
1 and 3 were computed considering both 13C and H NMR chemical
1
shifts and comparing them with the related experimental data. In
particular, since the available DP4+ Toolbox (Excel file) for the DP4+
computation allows the setting of sp3/sp2 atoms following the
“multistandard” approach, we used the chemical shift data set obtained
using TMS as reference compound (Table 2).
The conformers were optimized at the QM level using the
MPW1PW91 functional and the 6-31G(d) basis set.42 Experimental
solvent effects (MeOH) were reproduced using the integral equation
formalism version of the polarizable continuum model (IEFPCM).43
After this step at the QM level, the optimized geometries were visually
inspected in order to remove redundant conformers.
For compounds 1c and 3o, identified as the most probable
diastereoisomer of 1 and 3, respectively, Boltzmann-weighted
prediction of J values was performed for the most energetically
favored conformers [energies associated with the QM optimization
step, MPW1PW91/6-31G(d)], performing a two-step spin−spin
calculation (mixed keyword for Gaussian calculations) using the
MPW1PW91 functional and the 6-311+G(d,p) basis set.
Once the relative configurations of 1 and 3 were obtained, the
prediction of ECD spectra was performed using all the conformers
obtained from the DFT calculations and performing QM calculations
at the TDDFT (NStates = 40) MPW1PW91/6-31G(d,p) level, in
EtOH IEFPCM to reproduce the experimental solvent environment.
The final ECD spectra for both the enantiomers related to the
predicted stereoisomers of 1 and 3 (1c and 3o) were calculated
considering the influence of each conformer on the total Boltzmann
distribution taking into account the relative energies and were
graphically plotted using SpecDis software.44 In order to simulate
the experimental ECD curve, a Gaussian band-shape function was
applied with the exponential half-width (σ/γ) of 0.20 eV.
The perceived atropisomerism arising from the hindered rotation
about the biphenyl axis was evaluated by computing the rotational
energy barrier required for the interconversion between the
(aR*,8S*,9R*,10R*) and (aS*,8S*,9R*,10R*) atropisomers of com-
assuming that this system could be considered representative of all
diastereoisomers. Specifically, the starting geometry model represent-
ing the transition state was built with the two phenyl moieties
occupying the same plane, which was subsequently optimized at the
QM level using the Berny algorithm, the MPW1PW91 functional, and
the 6-31G(d) basis set followed by vibrational frequency calculations
(TS, CalcAll, Freq keywords for Gaussian calculations). Analysis of the
vibrational frequencies showed that the optimized structure was
correctly associated with the transition state, since the two phenyl
moieties slightly move along the biaryl axis, producing the two
different atropisomeric forms at each oscillation. Comparison of the
energies between the lowest energy-associated conformer found for
Lipid Peroxidation Measurement. Stock solutions of the
compounds and plant extract were made in 50% DMSO. The final
concentration of DMSO in the samples was lower than 0.05%, and in
all experiments its effects were determined.
I
J. Nat. Prod. XXXX, XXX, XXX−XXX