Conformational study of L-methionine and L-cysteine derivatives through quantum chemical calculations and 3JHH coupling constant analyses

Article abstract of DOI:10.3762/bjoc.13.94

The understanding of the conformational behavior of amino acids and their derivatives is a challenging task. Here, the conformational analysis of esterified and N-acetylated derivatives of L-methionine and L-cysteine using a combination of ¹H NMR and electronic structure calculations is reported. The geometries and energies of the most stable conformers in isolated phase and taking into account the implicit solvent effects, according to the integral equation formalism polarizable continuum model (IEF-PCM), were obtained at the ωB97X-D/aug-cc-pVTZ level. The conformational preferences of the compounds in solution were also determined from experimental and theoretical³ J_HH coupling constants analysis in different aprotic solvents. The results showed that the conformational stability of the esterified derivatives is not very sensitive to solvent effects, whereas the conformational equilibrium of the N-acetylated derivatives changes in the presence of solvent. According to the natural bond orbital (NBO), quantum theory of atoms in molecules (QTAIM) and noncovalent interactions (NCI) methodologies, the conformational preferences for the compounds are not dictated by intramolecular hydrogen bonding, but by a joint contribution of hyperconjugative and steric effects.

Full text of DOI:10.3762/bjoc.13.94

Conformational study of L-methionine and L-cysteine
derivatives through quantum chemical calculations
and 3JHH coupling constant analyses
Weslley G. D. P. Silva‡, Carolyne B. Braga*,‡ and Roberto Rittner
Full Research Paper
Open Access
Address:
Beilstein J. Org. Chem. 2017, 13, 925–937.
Chemistry Institute, University of Campinas, P.O. Box 6154,
doi:10.3762/bjoc.13.94
13083−970, Campinas, SP, Brazil
Received: 07 March 2017
Accepted: 27 April 2017
Published: 17 May 2017
Email:
Carolyne B. Braga* - carolyne.braga@iqm.unicamp.br
*
Corresponding author ‡ Equal contributors
Associate Editor: P. R. Schreiner
Keywords:
© 2017 Silva et al.; licensee Beilstein-Institut.
License and terms: see end of document.
amino acid derivatives; conformational analysis; cysteine; methionine;
NMR spectroscopy; quantum chemical calculations
Abstract
The understanding of the conformational behavior of amino acids and their derivatives is a challenging task. Here, the conforma-
tional analysis of esterified and N-acetylated derivatives of L-methionine and L-cysteine using a combination of 1H NMR and elec-
tronic structure calculations is reported. The geometries and energies of the most stable conformers in isolated phase and taking into
account the implicit solvent effects, according to the integral equation formalism polarizable continuum model (IEF−PCM), were
obtained at the ωB97X-D/aug-cc-pVTZ level. The conformational preferences of the compounds in solution were also determined
from experimental and theoretical 3JHH coupling constants analysis in different aprotic solvents. The results showed that the confor-
mational stability of the esterified derivatives is not very sensitive to solvent effects, whereas the conformational equilibrium of the
N-acetylated derivatives changes in the presence of solvent. According to the natural bond orbital (NBO), quantum theory of atoms
in molecules (QTAIM) and noncovalent interactions (NCI) methodologies, the conformational preferences for the compounds are
not dictated by intramolecular hydrogen bonding, but by a joint contribution of hyperconjugative and steric effects.
Introduction
Amino acids constitute the building blocks of proteins and high melting points, low vapor pressures and the occurrence of
peptides, which play an important role in numerous biological zwitterions in solution. Nevertheless, taking into account the
processes [1,2]. However, their studies in both isolated and recent experimental and theoretical developments, studies
condensed phases have been challenging for chemists and dealing with amino acids have been more widely reported,
physicists due to the particular amino acid properties, such as mainly in gas phase [3-8].
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Beilstein J. Org. Chem. 2017, 13, 925–937.
Among the 20 amino acids incorporated into proteins, phenylalanine and tyrosine [21], aspartic acid [22], proline [23]
L-methionine (L-Met) and L-cysteine (L-Cys) are the only two and histidine [24]. These studies have provided significant
containing sulfur. The former is an initiator amino acid in the results to understand the importance of the corresponding amino
protein synthesis of all eukaryotics cells [9], whereas disulfide acids in processes in which they take part in the polypeptide
bonds formed by the oxidized thiol groups of cysteine confer chain. Furthermore, these works presented unique explanations
exceptional stability for the peptides and proteins where they about the conformational preferences of amino acids.
are present [10]. Thus, a systematic study on the conformation-
al behavior of L-Met and L-Cys can reveal unique properties Therefore, it became of interest to extend the previous studies to
about the formation of proteins and peptides that happens in the investigate the conformational preferences of L-methionine and
biological environment.
L-cysteine esterified and N-acetylated derivatives (Table 1). In
order to obtain more insights about the main conformers and the
The conformers of L-Met and L-Cys have been investigated by operating effects in the compounds, both in isolated phase and
several experimental and theoretical methodologies, including in various aprotic solvents, 1H NMR spectroscopy and quan-
FTIR [11], rotational and IR−UV double resonance spectrosco- tum chemical calculations, including natural bond orbitals
pies [12,13], photon ionization mass spectrometry [14], X-ray (NBO), quantum theory of atoms in molecules (QTAIM), and
absorption [15] and quantum chemical calculations [16-19]. In noncovalent interactions (NCI) analyses were used.
spite of these many studies performed, there is still a lack of
Results and Discussion
information about the effects that rule their conformational
isomerism. Additionally, the conformational flexibility of both Esterified derivatives of L-Met and L-Cys
amino acids leads to a variety of low energy geometries, which The lowest-energy conformers of 1 and 2 and their calculated
make their studies even more difficult.
parameters (ωB97X-D/aug-cc-pVTZ) in gas phase and in solu-
tion (IEF−PCM) are shown in the Figure 1 and Table 2, respec-
An alternative capable of providing more detailed under- tively.
standing about the structure and properties of more complex
amino acids is the investigation of their esterified and N-acety- Each conformer of 1 and 2 (Figure 1) was named with a Roman
lated derivatives. These derivatives are soluble in several numeral followed by a letter (a, b or c). The number represents
organic solvents and thus, their properties can be studied the order of stability in chloroform for 1 and in isolated phase
through nuclear magnetic resonance (NMR), the most powerful for 2, while the letters denote the relationship between side and
spectroscopic characterization tool. For a deeper understanding main chains, which are illustrated on the Newman projections
of amino acid properties, an interplay between theoretical and of Figure 2. In the geometry a, hydrogen Ha is gauche to hydro-
experimental methods is crucial. Consequently, high-level gen atoms Hb1 and Hb2, while in the geometries b and c, Ha is
quantum chemical calculations, such as the Møller–Plesset anti to Hb2 and Hb1, respectively. These three possible disposi-
(
MP2) method and density functional theory (DFT) calcula- tions were built based on the dihedral angles Ha−C−C−Hb1 and
tions, together with experimental techniques have been Ha−C−C−Hb2 depicted in Table 2.
combined to achieve more accurate results [20-24].
The calculated populations (Table 2), derived from ΔE energies
Some amino acid derivatives have been recently studied by our for 1 and ΔG for 2, show that the most stable conformers of 1
research group, including the derivatives of tryptophan [20], and 2 are in the form b in both isolated phase and solution.
Table 1: Depiction of the studied compounds (1–4).
compound
R1
R2
R3
L-methionine ethyl ester (1)
CH2SCH3
SH
Et
Me
Et
H
L-cysteine methyl ester (2)
H
N-acetyl-L-methionine ethyl ester (3)
N-acetyl-L-cysteine methyl ester (4)
CH2SCH3
SH
COMe
COMe
Me
926

Beilstein J. Org. Chem. 2017, 13, 925–937.
Figure 1: Most stable conformers of 1 and 2 obtained theoretically at the ωB97X-D/aug-cc-pVTZ level.
Furthermore, the conformers b of the compound 1 are favored when the solvent is introduced. Using the IEF−PCM implicit
in the conformational equilibrium, since their populations solvent model, small changes in the populations of conformers
together are larger than 50% of the total population of 1, in all of 1 are observed when the solvent dielectric constant (ε) is in-
different studied media. Although the global minimum of 1 is in creased. However, these slight variations do not affect the total
the form b in gas phase and also in solution, the three more populations of conformers a, b and c, and thus, it is an indica-
stable geometries (1-IXb, 1-Xb and 1-XIb) in the former are tive that the conformers of 1 are not very sensitive to the sol-
substituted by three new structures (1-Ib, 1-VIIb and 1-VIIIb) vent effect.
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Beilstein J. Org. Chem. 2017, 13, 925–937.
Table 2: Calculated parameters (ωB97X-D/aug-cc-pVTZ) for the conformers of 1 and 2. Relative Gibbs free energy (ΔG) and electronic energy with
ZPE corrections (ΔE) are given in kcal mol−1, populations (P) in % and dihedral angles in degrees.
conformer
isolated
CHCl3
ΔE
CH2Cl2
CH3CN
DMSO
ΔE
dihedral angles
ΔE
P
P
ΔE
P
ΔE
P
P
Ha−C−C−Hb1 Ha−C−C−Hb2
1
-Ib
-IIa
-IIIb
-IVa
-Vc
-VIc
-VIIb
-VIIIb
-IXb
–
–
0.00
0.23
0.37
0.46
0.54
0.59
0.65
0.74
–
24.6
16.6
13.2
11.3
9.9
9.1
8.2
7.1
–
0.00
0.08
0.14
0.28
0.40
0.37
0.55
0.67
–
19.8
17.2
15.7
12.3
10.1
10.6
7.9
6.4
–
0.05
0.05
0.00
0.33
0.37
0.31
0.45
0.54
–
17.0
17.0
18.5
10.6
9.9
11.0
8.6
7.4
–
0.06
0.06
0.00
0.33
0.38
0.32
0.46
0.52
–
16.8
16.9
18.6
10.8
9.8
10.9
8.5
7.7
–
−57.48
64.78
−174.32
−51.15
−178.89
−50.56
65.24
1
1.38
1.97
1.99
2.04
2.27
–
5.2
2.0
1.9
1.7
1.2
–
1
−62.89
64.89
1
1
−179.14
−178.19
−59.02
−58.19
−67.20
−68.81
−68.81
1
66.45
1
−176.61
−175.66
176.11
174.67
174.67
1
–
–
1
0.00
0.70
0.66
53.9
16.4
17.7
1-Xb
–
–
–
–
–
–
–
–
1-XIb
–
–
–
–
–
–
–
–
ΔG
P
ΔG
P
ΔG
P
ΔG
P
ΔG
P
Ha−C−C−Hb1 Ha−C−C−Hb2
2
-Ib
-IIa
-IIIa
0.00
0.21
0.30
0.93
0.81
1.31
1.50
1.34
32.7
23.0
19.6
6.8
0.00
0.50
0.44
1.01
1.08
1.30
1.44
1.20
38.7
16.6
18.5
7.1
0.00
0.52
0.44
0.99
1.11
1.16
1.40
1.03
37.8
15.8
18.0
7.2
0.00
0.33
0.24
0.55
0.93
0.91
1.20
0.94
29.4
16.9
19.7
11.7
6.1
0.00
0.32
0.23
0.50
0.91
0.91
1.19
0.96
28.9
16.9
19.7
12.4
6.2
−64.21
59.63
65.19
64.87
61.72
−60.06
179.96
56.55
176.88
−59.75
−54.06
−114.09
−57.86
−179.39
61.62
2
2
2
-IVa
-Va
-VIb
-VIIa
-VIIIa
2
8.3
6.3
5.8
2
3.6
4.3
5.3
6.3
6.2
2
2.6
3.4
3.5
3.9
3.9
2
3.4
5.1
6.6
6.0
5.7
−63.06
Figure 2: Three possible dispositions presented by geometries of the analyzed compounds 1−4.
The same conformers were found in isolated phase and in solu- pling constants are almost constant in the studied solvents, sup-
tion for compound 2. Moreover, its four more stable geometries porting our findings through theoretical calculations that the
(
2-Ib, 2-IIa, 2-IIIa and 2-IVa) represent approximately 80% of conformational equilibria of 1 are not affected by the solvent
the conformational equilibrium (Table 2) in all different investi- change. The two different observed values for 3JHaHb1,obs
gated media. As well as for 1, geometries of 2 do not present (approximately 5.0 Hz) and 3JHaHb2,obs (approximately 7.0 Hz)
significant variations when ε is increased. It also demonstrates confirm that conformers in form b are favored in the equilib-
that the solvent effect does not affect the conformer popula- rium of 1, since these constants are dependent on the dihedral
tions of 2.
angle H−C−C−H, according to the well-known Karplus rela-
tionship [25].
To obtain more details about the solvent effect in the conforma-
tional isomerism of the studied compounds, experimental NMR As the observed 3JHH,obs coupling constant represents a
spectroscopy measurements and spin-spin coupling constant weighted average of the contribution of each conformer, the
(
3JHH) calculations were performed. The experimental 1H NMR calculated 3JHH,calc spin−spin coupling constant represents the
data for 1 (Table 3) indicate that the 3JHaHb1 and 3JHaHb2 cou- individual 3Ji coupling constant multiplied by the relative popu-
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Beilstein J. Org. Chem. 2017, 13, 925–937.
Table 3: Experimental and calculated 1H NMR data for the compound 1 in different solvents. The chemical shifts values are given in ppm and the
3JHH coupling constants in Hz.
solvent
ε
δHa
δHb1
δΗb2
3JHaHb1,obs
3JHaHb1,calc
3JHaHb2,obs
3JHaHb2,calc
CDCl3
CD2Cl2
4.8
9.1
4.00
3.97
3.84
3.55
2.24
2.22
2.09
1.89
2.17
2.14
2.09
1.78
5.1 ± 0.05
5.2 ± 0.05
6.1 ± 0.05
5.6 ± 0.05
4.6
4.8
4.7
4.7
7.1 ± 0.05
7.0 ± 0.05
6.1 ± 0.05
7.4 ± 0.05
7.5
7.3
7.4
7.4
CD3CN
DMSO-d6
37.5
46.7
lation (ni/nj) of each conformer i existent in the equilibrium, as In QTAIM analysis no bond path (BP) or bond critical point
shown by the Equation 1 [26]:
(BCP) are observed for the conformers of 1 and 2 between
atoms where an IHB was expected, indicating no presence of
IHB. Nevertheless, most conformers of 1 and 2 exhibit the NH2
group directed toward the oxygen atom of the carbonyl group
and thus, an attractive interaction NH…O=C characteristic of an
(1)
In this way, the averaged 3JHaHb1,calc and 3JHaHb2,calc (Table 3) IHB would be expected. On the basis of some studies where
obtained for the conformers of 1 are in good agreement with the QTAIM fails in describing the presence of weak long-range
experimental ones and reproduce well the results observed for bonds [27,28], the NCI analysis was also performed. A compar-
this compound.
ison between the QTAIM and NCI analyses for conformers of 1
and 2 is presented in Figure S1 in Supporting Information
The study of 2 through NMR spectroscopy was not carried out File 1.
in the present work because it was not possible to obtain the
corresponding free amino acid derivative. When in solution, Although the QTAIM molecular graphs (Figure S1-a) do not
cysteine forms a dimer through disulfide bonds between the display any BP or BCP related to an IHB for the studied geome-
–
SH groups and thus, it cannot be compared to the theoretically tries, the NCI analysis shows that most of the stable conformers
proposed compound. Another alternative would be the use of present a NH…O=C-type attractive interaction, except the
some chemical agent to break the disulfide bond in 2, but it geometries 1-IIIb, 2-IIa, and 2-VIIa. This interaction can be
could induce changes in the conformational isomerism. Howev- visualized through the NCI isosurfaces (Figure S1-b) and the
er, the level of theory (ωB97X-D/aug-cc-pVTZ) used in this plot of the reduced density gradient S versus sign (λ2)ρ(r)
work for the studied compounds has shown good results for (Figure S1-c). Thus, the IHB NH…O=C found was character-
other amino acid derivatives, when comparing theoretical with ized by trough with λ2 < 0 and the presence of a blue color in
experimental data [22-24]. Although 2 could not be experimen- the sphere between the H(N) and O(C) atoms [29]. On the con-
tally studied, the theoretical calculations carried out strongly trary, the non-observation of this interaction through QTAIM
suggest that the conformational equilibrium of 2 and the popu- analysis is explained by the fact that troughs with λ2 < 0 do not
lations of its conformers are not very sensitive to solvent effect. reach S = 0, as described by Lane and co-workers [28].
When it comes to the study of amino acids and their derivatives, The presence of the IHB NH…O=C was also investigated by the
some studies found in the literature explain the conformational use of NBO analysis. The NBO calculations (Table 4) indicate
stability of amino acids solely by the formation of an intramo- that an IHB occurs in the conformers 1-Ib, 1-VIIb, 1-VIIIb and
lecular hydrogen bonding (IHB) [2,8,13]. Thus, to investigate 2-IVa, because only these mentioned geometries present the
the responsible effects governing the stability of the conformers hyperconjugative nO→σ*N–H interaction. However, as these
of 1 and 2, QTAIM, NCI and NBO methodologies were em- interactions are of small magnitude (0.72, 0.94, 0.86 and
ployed. These analyses were performed only for conformers 1.32 kcal mol−1, respectively) and the other low-energy struc-
that exist in solution.
tures do not exhibit any significant nO→σ*N–H interaction, it is
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Beilstein J. Org. Chem. 2017, 13, 925–937.
Table 4: Calculated NBO parameters (ωB97X-D/aug-cc-pVTZ) for the most stable conformers of the compounds 1 and 2. Relative energy of the
steric (Erel,Lewis) and hyperconjugative (Erel,Hyper) interactions are given in kcal mol−1. The sum of Erel,Lewis and Erel,Hyper is the total energy of the
system.
conformer
CHCl3
DMSO
nO→σ*N–H a
Erel,Lewis
Erel,Hyper
Erel,Lewis
Erel,Hyper
1
-Ib
-IIa
-IIIb
-IVa
0.89
1.84
2.02
4.04
0.00
1.23
0.18
0.54
1.66
2.44
2.63
4.42
0.22
1.14
0.00
0.38
1.76
1.92
2.32
4.02
0.00
0.91
0.25
0.38
2.27
2.51
3.03
4.51
0.21
0.96
0.00
0.31
0.72
−
1
1
−
1
−
1-Vc
−
1-VIc
−
1-VIIb
0.94
0.86
1
-VIIIb
2
-Ib
0.00
2.05
4.31
6.38
3.59
2.14
3.73
4.44
0.00
2.11
4.33
5.97
2.95
1.26
2.95
3.73
1.74
4.76
6.26
5.84
7.62
0.00
6.22
7.30
2.76
5.98
7.48
6.69
8.03
0.00
6.43
7.70
−
−
2-IIa
2-IIIa
−
2
2
-IVa
1.32
−
2-Va
-VIb
−
2-VIIa
−
2
-VIIIa
−
aNBO calculations were realized with an energy threshold of 0.5 kcal mol−1.
possible to conclude that IHB is not the main governing effect The calculated parameters (Table 5) indicate that the most
of the conformational preferences of compounds 1 and 2.
stable conformers of 3 (3-trans-Ia) and 4 (4-trans-Ia) are trans
in all different studied media. In isolated phase, the conformer
The contributions of steric (Erel,Lewis) and hyperconjugative 3-trans-Ia represents 45.6% of the conformational equilibrium
Erel,Hyper) effects (Table 4) indicate that the most destabilized of 3, but when the dielectric constant of the medium is in-
(
conformers by steric hindrance are also the most stabilized ones creased, this geometry is destabilized and has its population de-
by hyperconjugation, such as the conformers 1-Ib and 2-Va. In creased to 34.8%. The same tendency is observed for 4-trans-
this way, the NBO investigation shows that not only is a Ia, which has its population reduced from almost 100% in iso-
specific interaction the responsible for the observed lated phase to 67.7% in DMSO. In general, these population
conformational preferences for the compounds 1 and changes for the geometries of compounds 3 and 4 indicate that
2
, but an interplay between hyperconjugation and steric their conformational equilibria are sensitive to solvent effects.
hindrance.
The conformational changes induced by the solvent were also
N-Acetylated derivatives of L-Met and L-Cys
investigated through experimental 3JHH coupling constant ob-
A similar study was performed for the derivatives 3 and 4. The tained from 1H NMR spectroscopy and the corresponding
most stable conformers of 3 and 4 and their calculated parame- calculated ones (Table 6). For the compound 3, the experimen-
ters (ωB97X−D/aug−cc−pVTZ) in isolated phase and in solu- tal data show that the 3JHaHb1,obs and 3JHaHb2,obs coupling con-
tion are shown in Figure 3 and Table 5, respectively.
stants vary when the dielectric constant of the solvent (ε) is in-
creased, corroborating the theoretical findings that the popula-
Each conformer of 3 and 4 was named with the cis−trans desig- tions of its conformers are sensitive to the solvent effects. In
nation, which indicates the position of the amide linkage with chloroform, the difference between 3JHaHb1,obs and 3JHaHb2,obs
respect to the C(O)OEt group in 3 and C(O)OMe in 4, followed (about 2.0 Hz) indicates that conformers a are favored in this
by a Roman numeral and a letter. The number represents the solvent, as expected (54.9% from Table 5). When ε is increased,
order of stability in chloroform, and the letter denotes the rela- the difference between 3JHaHb1,obs and 3JHaHb2,obs increases to
tionship between side and main chains (Figure 2). The presence almost 4.0 Hz in DMSO and this fact is related to the stabiliza-
of a larger number of dihedral angles in the compound 3 implies tion of conformers c, which have Ha anti to Hb1, and gauche to
the existence of more stable conformers than 4.
Hb2 (Table 5). Unlike 3, the 3JHaHb1,obs and 3JHaHb2,obs for
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Beilstein J. Org. Chem. 2017, 13, 925–937.
Figure 3: Most stable conformers of 3 and 4 obtained theoretically at the ωB97X-D/aug-cc-pVTZ level.
compound 4 exhibit close values in CHCl3 (3.9 and 4.3 Hz, re- conformers a of 4 being more populated in all studied media,
spectively), and this also suggests the predominance of 3JHaHb2,obs increases from 4.3 Hz in CDCl3 to 7.5 Hz in
conformers a in this less polar solvent. However, despite DMSO, and it indicates the stabilization of conformers b in
Table 5: Calculated parameters (ωB97X-D/aug-cc-pVTZ) for conformers of 3 and 4 in isolated phase and in solution (IEF−PCM). Relative Gibbs free
energies (ΔG) and electronic energies with ZPE corrections (ΔE) are given in kcal mol−1, populations (P) in %, and dihedral angles in degrees.
conformer
isolated
CHCl3
ΔE
CH2Cl2
CH3CN
DMSO
ΔE
dihedral angles
ΔE
P
P
ΔE
P
ΔE
P
P
Ha−C−C−Hb1 Ha−C−C−Hb2
3
-trans-Ia
-trans-IIc
-trans-IIIc
-trans-IVc
-trans-Vb
-cis-VIa
-trans-VIIc
-trans-VIIIc
0.00
1.44
–
45.6
4.0
–
0.00
0.60
1.11
1.24
1.00
–
54.9
19.9
8.4
6.7
10.1
–
0.00
0.51
0.84
0.99
1.00
1.13
–
45.7
19.4
11.0
8.5
8.6
6.8
–
0.00
0.16
0.68
0.73
1.00
0.98
–
36.4
27.6
11.6
10.5
6.8
7.1
–
0.00
0.13
0.66
0.60
1.00
0.96
–
34.8
27.8
11.3
12.7
6.5
6.9
–
62.03
174.83
175.55
177.18
69.28
−53.73
−69.51
−67.86
−66.41
184.60
−53.08
−64.16
−60.85
3
3
3
–
–
3
1.07
–
7.4
–
3
62.43
3
0.41
0.49
22.9
20.1
–
–
179.17
-177.35
3
–
–
–
–
–
–
–
–
ΔG
P
ΔG
P
ΔG
P
ΔG
P
ΔG
P
Ha−C−C−Hb1 Ha−C−C−Hb2
4
-trans-Ia
0.00
2.17
3.79
3.87
97.2
2.5
0.00
1.21
2.68
2.72
87.0
11.2
0.9
0.00
0.98
2.68
2.42
82.0
15.7
0.9
0.00
0.57
2.47
1.98
69.7
26.8
1.1
0.00
0.51
2.47
1.93
67.7
28.7
1.1
62.60
−56.64
−62.18
−164.09
−55.56
−175.04
178.85
77.48
4-trans-IIb
4-trans-IIIb
0.2
4-trans-IVc
0.1
0.9
1.4
2.4
2.5
931

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Table 6: Experimental and calculated 1H NMR data for the compounds 3 and 4 in different solvents. The chemical shifts values are given in ppm and
the 3JHH coupling constants in Hz.
compound
solvent
ε
δΗ(N) δHa
δHb1 δΗb2 3JHaHb1,obs 3JHaHb1,calc 3JHaHb2,obs 3JHaHb2,calc 3JHaH(N)
CDCl3
CD2Cl2
CD3CN
4.8
9.1
6.18
6.18
6.70
8.26
4.70
4.62
4.45
4.31
2.17
2.13
2.03
1.92
1.98 7.1 ± 0.07
1.95 7.7 ± 0.07
1.89 8.6 ± 0.07
1.84 9.1 ± 0.07
7.0
7.3
8.1
8.2
5.1 ± 0.07
5.1 ± 0.07
4.9 ± 0.07
4.9 ± 0.07
4.0
3.9
3.7
3.7
7.0 ± 0.07
5.5 ± 0.07
–
3
37.5
DMSO-d6 46.7
7.4 ± 0.07
CDCl3
CD2Cl2
CD3CN
4.8
9.1
6.43
6.47
6.84
8.32
4.90
4.83
4.62
4.44
3.03
3.00
2.91
2.83
3.00 3.9 ± 0.05
2.98 4.3 ± 0.05
2.86 4.8 ± 0.05
2.74 5.0 ± 0.05
3.1
3.2
3.5
3.9
4.3 ± 0.05
4.4 ± 0.05
6.0 ± 0.05
7.5 ± 0.05
4.1
4.4
6.3
6.6
7.8 ± 0.05
7.5 ± 0.05
7.9 ± 0.05
7.6 ± 0.05
4
37.5
DMSO-d6 46.7
more polar solvents, which have Ha anti to Hb2. Overall, the interactions. Similarly to the results obtained for the com-
averaged 3JHH,calc coupling constants obtained for the pounds 1 and 2, these interactions are of small magnitude (Ta-
conformers of 3 and 4 (Table 6) are in a good agreement with ble 7), and their presence is not related to the order of energy
the experimental data and both reproduce well the observed observed for the studied conformers, indicating that the IHB
trend for these compounds.
does not play a major role in the stability of the conformers of 3
and 4. Also analogously to 1 and 2, the conformational prefer-
Aiming to explain the higher stabilities showed by the ences observed for the conformers of the N-acetylated deriva-
conformers 3-trans-Ia and 4-trans-Ia in all studied media, tives result from an interplay between steric repulsion and
QTAIM, NCI, and NBO approaches were carried out for the hyperconjugation.
conformers of 3 and 4 existing in solution (Figure 4 and
Figure 5). For example, in QTAIM analysis for the conformers Conclusion
of 4 (Figure 5a), a BP and a BCP regarding the IHB were ob- In summary, the use of quantum chemical calculations and 3JHH
served only for 4-trans-IIb and 4-trans-IVc, demonstrating the coupling constant analyses, in the present work, allowed the de-
presence of a S−H…O−like IHB and, consequently, the forma- termination of the conformational preferences of methionine
tion of a six and seven−membered ring, respectively. In agree- and cysteine esterified and N−acetylated derivatives in isolated
ment with the QTAIM, NCI methodology (Figure 5b and phase and in different aprotic solvents. A comparison between
Figure 5c) confirms the presence of this S−H…O interaction in calculated and experimental 3JHH coupling constants indicated
the conformers 4-trans-IIb and 4-trans-IVc (λ2 < 0 in the NCI that the conformational isomerism of compounds 1 and 2 is not
plot, and a blue color in the sphere between the carbonyl very sensitive to solvent effects. On the other hand, the
oxygen and the H(S) atom in the NCI isosurface). In addition, conformers of 3 and 4 had their populations changed when the
NCI analysis also indicates the presence of an IHB NH…O=C solvent effects were taken into account.
(
not observed in QTAIM) in conformers 3-trans-Ia, 3-trans-
Vb, 4-trans-Ia, and 4-trans-IIb.
NBO, QTAIM and NCI methodologies showed that the pres-
ence of a NH…O=C−like IHB in some of the studied
In order to evaluate also the presence of IHB, as well as the conformers is not related to their stabilities and, thus, more than
influences of steric and hyperconjugative interactions on the just a specific interaction is governing the conformational
conformational isomerism of 3 and 4, NBO analysis was em- isomerism of the compounds 1, 2, 3, and 4. The observed
ployed. The NBO calculations (Table 7) confirm the presence conformational preferences for these derivatives are due
of IHB in conformers 3-trans-Ia, 3-trans-Vb, and 4-trans-Ia, to a combination of steric hindrance and hyperconjugative
evidenced by the nO→σ*N–H and nO→σ*S–H hyperconjugative effects.
932

Beilstein J. Org. Chem. 2017, 13, 925–937.
Figure 4: (a) QTAIM molecular graphs [30]; (b) NCI isosurfaces generated with S = 0.6 au and blue−green−red scaling from
0.02 < (λ2)ρ(r) < 0.02 au, and (c) NCI plots of the reduced density gradients S versus sign (λ2)ρ(r) for the conformers of 3.
−
933

Beilstein J. Org. Chem. 2017, 13, 925–937.
Figure 5: (a) QTAIM molecular graphs; (b) NCI isosurfaces generated with S = 0.6 au and blue−green−red scaling from −0.02 < (λ2)ρ(r) < 0.02 au,
and (c) NCI plots of the reduced density gradients S versus sign (λ2)ρ(r) for the conformers of 4.
To sum up, the obtained results in the present study are a good Spectroscopic measurements
illustration of the nature of amino acids derivatives in solution. 1H NMR spectra for 1, 3 and 4 were recorded on a Bruker
Furthermore, these results can be extended to the understanding Avance III operating at 600.17 MHz for hydrogen nuclei. Com-
of the conformational behavior of methionine and cysteine pound 2 was not experimentally studied, since it dimerized
amino acid in the biological environment, such as in polypep- during the measurements to give the corresponding disulfide de-
tide chains.
rivative. Spectra were acquired using solutions of ca. 10 mg of
solute in 0.7 mL of deuterated solvents (CDCl3, CD2Cl2,
CD3CN and DMSO-d6), referenced to internal TMS. Typical
acquisition and processing conditions are shown in the NMR
Experimental
Synthesis of compounds 1, 3 and 4
Compound 1 was purchased from Sigma-Aldrich in the form of spectra provided in Supporting Information File 1 (Figures
chloridrate and deprotonated using activated zinc dust, as de- S2–S13).
scribed in the literature for similar compounds [31]. Com-
pounds 3 and 4 were obtained by the esterification of the corre- Computational details
sponding N-acetyl-L-amino acids (Sigma-Aldrich), following a The starting conformer geometries for 1 and 2 were constructed
known procedure [23,32]. The detailed syntheses are described from the six most stable optimized conformers of L-alanine
in Supporting Information File 1.
methyl ester (Ala-OMe), reported by a previous study [33],
934

Beilstein J. Org. Chem. 2017, 13, 925–937.
Table 7: NBO parameters for conformers of compounds 3 and 4, calculated at the ωB97X-D/aug-cc-pVTZ level of theory. Relative energy of the
steric (Erel,Lewis) and hyperconjugative (Erel,Hyper) interactions are given in kcal mol−1. The sum of Erel,Lewis and Erel,Hyper is the total energy of the
system.
conformation
CHCl3
DMSO
nO→σ*N–H a
nO→σ*S–H a
Erel,Lewis
Erel,Hyper
Erel,Lewis
Erel,Hyper
3
-trans-Ia
-trans-IIc
-trans-IIIc
-trans-IVc
-trans-Vb
7.47
3.13
1.17
0.00
3.85
–
8.65
3.63
1.44
0.00
3.75
–
5.19
3.11
0.16
0.00
0.92
4.63
5.90
3.91
0.35
0.00
0.39
4.12
0.98
–
–
–
–
–
–
–
3
3
–
3
–
3
0.70
–
3
-cis-VIa
4
-trans-Ia
2.32
0.00
3.86
5.26
2.72
0.00
1.63
3.24
3.14
0.00
5.94
7.15
2.54
0.00
2.51
4.99
1.03
–
–
4-trans-IIb
–
–
–
4-trans-IIIb
–
4-trans-IVc
0.86
aNBO calculations were realized with an energy threshold of 0.5 kcal mol−1.
which have the less energetic arrangement of the backbone [41] functionals, and the ab initio MP2 method [42], with the
CH3−O−C(O)−CH(NH2)−], as follows. A methyl hydrogen aug-cc-pVTZ basis set [43], in order to achieve accurate energy
[
atom (side chain) of Ala-OMe was substituted by CH2−S−CH3 and geometry results and at a reasonable computational cost.
and S−H, giving rise to six new geometries for the compounds 1 Since the ωB97X-D/aug-cc-pVTZ level presented one of the
and 2, respectively. Moreover, for 1, at the beginning of the smallest mean absolute deviation from MP2/aug-cc-pVTZ
backbone a methyl group was added to the Ala-OMe structures single point calculations (Table S1, Supporting Information
by replacing a hydrogen atom of their methyl groups. Thus, six File 1), assumed as the reference level, and as the ωB97X-D
potential energy curves (PEC’s) for 1 and six potential surfaces DFT functional has been recognized to reliably treat noncova-
(
PES, Figure S14 of Supporting Information File 1) for 2 were lent interactions as well as to present good proximity with spec-
built from these six new structures of the compounds by scan- troscopic results [22-24], it was used in all subsequent calcula-
ning all torsional angles of the side chain (Figure 6) in 36 steps tions. These calculations were only performed for the
of 10° each, from 0° to 360°, at the B3LYP/cc-pVDZ level. In conformers of 2 due to their size compared to the geometries of
this step, the dihedral angles of the backbone were kept fixed. the L-Met esterified derivative. Then, beyond the conformers of
3
8 and 34 different energy minima were identified for 1 and 2, the compound 2, the conformers of 1 were also fully optimized
respectively.
at the ωB97X-D/aug-cc-pVTZ level in both isolated phase and
implicit solvent (chloroform, dichloromethane, acetonitrile, and
dimethyl sulfoxide), according to the Integral Equation
Formalism Polarizable Continuum Model (IEF−PCM) [44]. As
expected, the ωB97X-D/aug-cc-pVTZ theoretical level showed
good performance for these derivatives in comparison to simi-
lar systems previously studied [12,17,19], where higher levels
of theory were used. These optimization calculations resulted in
1
1 stable conformers for 1 and in 8 for 2, which were taken into
account in the discussion of the results. The other geometries,
with relative energies over 2.0 kcal mol−1, were discarded
because they do not contribute to the conformational equilib-
rium of the studied compounds. Frequency calculations with
ZPE corrections were carried out to guarantee the absence of
imaginary frequencies in the geometries. Spin-spin coupling
Figure 6: Definition of the selected dihedral angles for the studied
compounds.
The 34 geometries of 2 were fully reoptimized without restric- constants (3JHH) were calculated for each conformer in the
tions using the B3LYP [34,35], B3LYP-D3 [36], CAM-B3LYP IEF−PCM model using the ωB97X-D functional and EPR-III
[
37], M05-2X [38], M06-2X [39], B97-D [40] and ωB97X-D (for C and H atoms) [45] and aug-cc-pVTZ [43] (for O, N and S
935

Beilstein J. Org. Chem. 2017, 13, 925–937.
3
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Blanco, S.; Sanz, M. E.; López, J. C.; Alonso, J. L.
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using the Gaussian 09 program [46].
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Possible intramolecular interactions were evaluated through
natural bond orbital (NBO) analysis, at ωB97X-D/aug-cc-pVTZ
level, using NBO 5.9 program [47]. In addition, quantum theory
of atoms in molecules (QTAIM) [48] and noncovalent interac-
tions (NCI) [49] analyses were carried out for the same purpose
using the AIMALL [50] and NCIPLOT [29] programs, respec-
tively.
5. Alonso, J. L.; Pérez, C.; Sanz, M. E.; López, J. C.; Blanco, S.
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1
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1
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Prince, K. C.; Carravetta, V. J. Electron Spectrosc. Relat. Phenom.
QTAIM and NCI molecular graphs for the most stable
conformers of compounds 1 and 2; 1H NMR spectra for the
studied compounds; potential energy surfaces and contour
maps for the L-cysteine methyl ester; comparison of the
energies, populations and other relevant structural
parameters for the conformers of the L-cysteine methyl
ester in several theoretical levels; detailed procedures for
preparation of the compounds.
2
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The authors thank São Paulo Research Foundation (FAPESP,
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C.B.B. #2012/18567-4). Thanks also to Conselho Nacional de
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