Analysis of crystallographic structures of Ni(II) complexes of α-amino acid Schiff bases: Elucidation of the substituent effect on stereochemical preferences

Article abstract of DOI:10.1039/c7dt00014f

In this study, we performed critical analysis of 13 crystallographic structures of various Ni(ii) complexes of amino acid Schiff bases. The major finding of this work is the significance of a parallel displaced type of aromatic interactions between o-amino-benzophenone and Pro N-benzyl rings. The quality of these aromatic interactions was shown to control the steric environment around the amino acid side-chain, rendering variously substituted Ni(ii) complexes of different thermodynamic stabilities. The discovered structural trend holds true for aliphatic, aromatic and sterically bulky amino acids and can be used for the rational design of new and more efficient chiral ligands for general asymmetric synthesis of tailor-made α-amino acids.

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Efficient extraction of sulfate from water using
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Analysis of crystallographic structures of Ni(II) complexes of α-
amino acid Schiff bases; Elucidation of the substituents effect on
stereochemical preferences
Received 00th January 20xx,
Accepted 00th January 20xx
Yong Nian,a,b Jiang Wang,a,b Hiroki Moriwaki,c Vadim A. Soloshonok*d,e and Hong Liu*a,b
DOI: 10.1039/x0xx00000x
www.rsc.org/
In this study, we performed critical analysis of the 13 crystallographic structures of various Ni(II) complexes of amino acid
Schiff bases. The major finding of this work is the significance of a parallel displaced type of aromatic interactions between
the o-amino-benzophenone and the Pro N-benzyl rings. The quality of these aromatic interactions was shown to control
the steric environment around the amino acid side-chain, rendering variously substituted Ni(II) complexes of different
thermodynamic stability. The discovered structural trend holds true for aliphatic, aromatic and sterically bulky amino acids
and can be used for the rational design of new and more efficient chiral ligands for general asymmetric synthesis of tailor-
made α-amino acids.
in the development of general methods for synthesis of fluorine,5
phosphorus contacting,6 sterically constrained,7 bis-AAs8 and
Introduction
The residues of tailor-made amino acids (AAs)1 are becoming an
increasingly common structural trait among top-selling and most
prescribed life-saving pharmaceuticals. In fact, among the drugs
introduced to the market in the last decade, over 20% contain at
least one tailor-made AA incorporated into a peptide chain.2
Consequently, the need for advanced approaches to
enantiomerically pure AAs is at an all-time high, satisfying the
growing demand for structurally and functionally novel types of
tailor-made AAs.3,4 For quite some time, our groups were interested
heterocyclic AAs.9 Along with many other research groups,10 we
were particularly interested in advancing the chemistry of Ni(II)
complexes of AAs derived Schiff bases11 as a general methodology
for preparation of α-12 and β-AAs.13 Since the seminal work by
Belokon et al.,14 introducing proline-derived glycine Schiff base
complex 1a (Scheme 1), there have been numerous attempts to
modify the structure of 1a10,15 with the aim to improve its
stereocontrolling properties. In particular, numerous derivatives of
1, bearing Me, F, Br, Cl, NO2 on the proline N-benzyl group and o-
amino-benzophenone moiety, were designed16,17 and used for
asymmetric synthesis of AAs. For example, as shown in Scheme 1,
methylation of complexes 1a-1h with MeI in the presence of base,
results in the formation of two diastereomeric complexes (S)(2S)-2
and (S)(2R)-3. While the reported diastereoselectivities of the
alkylation are varying from one paper to another, one can clearly
perceive an unambiguous trend, that the diastereoselectivity of the
methylation of derivatives 1b-1h is greater (90%-99% de) as
compared to that of the reaction of unsubstituted Gly complex 1a
(85%-90% de).11
a.CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica,
Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
b.University of Chinese Academy of Sciences
100049, China
E-mail: hliu@simm.ac.cn
，No.19A Yuquan Road, Beijing
c. Hamari Chemicals Ltd., 1-4-29 Kunijima, Higashi-Yodogawa-ku, Osaka 533-
0024,Japan
d.Department of Organic Chemistry I, Faculty of Chemistry, University of the Basque
Country UPV/EHU, Paseo Manuel Lardizábal 3, 20018 San Sebastián, Spain
e. IKERBASQUE, Basque Foundation for Science, Maria Diaz de Haro 3, 48013 Bilbao,
Spain
E-mail: vadym.soloshonok@ehu.es
Electronic Supplementary Information (ESI) available: The preparative procedure, 1H
and 13C NMR spectra and X-ray structure analyses (PDF). CCDC 1520061, 1520062,
1520063, 1400951, 1422992 contains the supplementary crystallographic data for this
paper. These data can be obtained free of charge via
www.ccdc.cam.ac.uk/data_request/cif. See DOI: 10.1039/x0xx00000x
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Results and discussion
Structures of Gly Schiff base Ni(II) complexes 1a and 1b
To begin our study, we decided to scrutinize the crystallographic
structures of the corresponding Gly Ni(II) complexes 1a and 1b. X-
ray data for complex 1a, derived from the unsubstituted ligand 4a,
were previously published, however, have never been discussed
from the standpoint of non-bonding interactions determining its 3D
profile. Complex 1b, prepared (Scheme 2) from tri-chloro-ligand 4b,
is a new compound and its synthesis, full characterization and X-ray
data, are reported in this work for the first time.
Scheme 1 Methylation of unsubstituted 1a and various substituted
Gly complexes 1b-1h.
Validity of this trend is strongly supported by the successful design
of tri-Cl substituted Gly complex 1b, which turned out to be the
best performing derivative, providing up to >99% de of major
diastereomers.17 On the other hand, the rationale behind this
notable substituent effect is far from obvious, still waiting for an
adequate explanation. The major obstacle in validation of the
observed trend is that the substituents on the proline N-benzyl
group and/or o-amino-benzophenone moiety are located too far
from the glycine moiety and simply cannot have any direct
electronic or steric effect on the stereochemical outcome.
Consequently, we posited that the substituents might influence the
“secondary” 3D-structure of the corresponding Ni(II) complexes,
such as a position of the N-benzyl group or its interactions with o-
amino-benzophenone moiety, which in turn, can lead to the
structural changes in the Ni(II) chelating rings, including the amino
acid Schiff base residue. In this work, we present detailed analysis
of new as well as previously published crystallographic data of ten
Ni(II) complexes derived from Schiff bases of glycine, alanine and
several other amino acids, which quite reasonably confirm our
original assumption. In particular, we demonstrate that aromatic
stacking interactions between the proline N-benzyl group and the
phenyl rings of the benzophenone moiety is the major structural
feature of the Ni(II) complexes. These attractive, noncovalent
interactions between aromatic rings lead to a distinct puckering of
the Ni(II) chelate rings, which, in turn, result in different
stereochemical environment around the amino acid residue. The
provided in this work structural analysis and conclusions have a
predictive power and can be used for rational design of new chiral
ligands general asymmetric synthesis of tailor-made α- and β-AAs.
Scheme 2 Synthesis of Gly Schiff base complexes 1a and 1b from
ligands 4a and 4b.
Analysis of crystallographic structure of Gly complex 1a (Figure 1)
shows no obvious aromatic-aromatic interactions, as the nearest
distance between the o-hydrogen of the benzophenone phenyl ring
and the p- and m-carbons of the benzyl group, are 4.32 Å (H23…C19)
and 4.30 Å (H23…C18), respectively, and beyond the range of
aromatic staking interactions.18 On the other hand, the benzyl
phenyl is skewed towards the glycine carbonyl and the structure is
apparently stabilized by electrostatic attractive interactions
between the benzyl o-hydrogen and the C=O; 2.95 Å (H17…C1)and
2.83 Å (H17…O2), respectively.
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C
N
O
Cl
Ni
1b
1a
Fig. 2 Deviation from the planarity of the Ni(II) coordination sphere
in Gly complexes 1a and 1b.
In both compounds 1a and 1b, the chelate rings around the Ni(II)
are far from planar structure displaying some distinct puckering. For
example, as can be seen form Figure 2, while the N-Ni-O angles are
closer to the ideal 180o, the N-Ni-N bonding is more pronouncedly
bent showing 168.97o and 173.42o, respectively. However, to
accommodate the phenyl-carbonyl in 1a, and the phenyl-phenyl
interactions in 1b, the direction of bending is just opposite, up and
down, respectively. More detailed analysis of the chelate rings
reveals also striking differences in the stereochemistry of the
1b
1a
Cl
Ni
Cl
N
O
N
O
N
N
O
O
Ni
O
N
O
N
Cl
1b
1a
chelate rings (refers to axial chirality of the chelate rings
in Gly complexes 1a and 1b in Figure 3 and dihedral
angles of the chelate rings around the Ni(II) in Gly
complexes 1a and 1b in Figure 4).
Fig. 1 Crystallographic structures of Gly Schiff base Ni(II) complexes
(S)-1a and (S)-1b.
In sharp contrast to 1a, the crystallographic structure of 1b (Figure
1) reveals explicit interaction between the o-amino-benzophenone
and benzyl rings, which can be defined as a mixed case of parallel
displaced19 and T-shaped or edge-to-face20 electrostatic aromatic
interactions.21 Thus, the distances between the o-hydrogen and
chlorine-bearing m- and p-carbons are only 2.99 Å (H8…C20) and
3.25 Å (H8…C19). Furthermore, the structure might be additionally
stabilized by the attractive electrostatic interactions between the
benzyl chlorine atoms and the corresponding o- (Cl3…H8, 3.30 Å)
and m-hydrogens (Cl2…H7, 3.55 Å) of the benzophenone ring.
Unambiguous support for the Cl-H attractive electrostatic Fig. 3 Axial chirality of the chelate rings in Gly complexes 1a and 1b.
interactions22 comes from the presence of the intermolecular short Thus, the phenyl-carbonyl and the phenyl-phenyl interactions-
contact (2.93 Å) observed between the benzyl p-chlorine atom of induced puckering of the chelate rings in 1a and 1b, gives rise to the
one molecule of 1b and the m-hydrogen of the benzophenone ring axial chirality along the Ni-N (Schiff base) and Ni-N (amide) bonds.
of another.
Remarkably, as presented in Figure 3, the absolute configuration of
These striking differences between 3D structures of 1a and 1b have these chiral axes is again, exactly opposite.
also a profound reflection in the arrangements of the Ni(II) chelate Similarly striking differences can also be seen in the dihedral angles
rings.
of the chelate rings, as shown in Figure 4.
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Å), well within an average range (3.3-3.8 Å) of aromatic staking
interactions.18
Fig. 4 Dihedral angles of the chelate rings around the Ni(II) in Gly
complexes 1a and 1b.
As one can see form Figure 4, while the absolute values of the
dihedral angles are differing the corresponding signs are opposite
as a consequence of the phenyl-carbonyl in 1a, and the phenyl-
phenyl interactions in 1b. Thus, in the case of 1a, the glycine moiety
is up, to place the carbonyl in close proximity to the benzyl group,
pushing the six- and five-membered rings, correspondingly, down
and up. By contrast, the interactions between the benzyl and o-
amino-containing phenyl ring of the benzophenone moiety, brings
the six-membered ring up and the five-membered rings down.
Considering these special arrangements of Gly complexes 1a and 1b,
we can draw a major conclusion that the presence of substituents
of the benzyl and benzophenone phenyl groups can indeed have a
profound effect on the 3D structure of these Ni(II) complexes. The
effect can be reasonably rationalized by the substituent-induced
preferences for the electrostatic aromatic interactions shaping up
the Ni(II) coordination sphere and other facets of structural features.
The discovered structural aspects of Gly complexes 1a and 1b are
quite exciting and of profound general importance for the major
objective of this work, analysis of the crystallographic structures of
Ala complexes 2a-2h.
Fig. 5 Crystallographic structures of Ala Schiff base Ni(II) complexes
(S)(2S)-2a and (S)(2S)-2b.
Such a dramatic reverse in the preferences of aromatic interactions
can be explained by the fact that the up-down-up arrangement of
the chelate rings in 1a cannot accommodate the alanine moiety,
due to close proximity between the pro-S proton and the
benzophenone phenyl ring (2.68 Å). On the other hand, the
observed down-up-down system, makes a room for the methyl
group, pointing down, relatively to the Ni(II) coordination sphere.
Crystallographic structure of Ala complex 2b, has a similar, parallel
displaced type of interactions between the o-amino-benzophenone
and benzyl rings. However, in the case of 2b, these interactions
appear to be of much greater quality as the two aromatic rings are
nearly parallel to each other, measuring distances between C/H
atoms about 3.4-3.7 Å. Apparently, similar to Gly 1b, the aromatic
interactions in Ala 2b are additionally stabilized by the attractive
electrostatic interactions between the chlorine atoms and the
corresponding m-hydrogens (Cl2…H8, 3.60 Å and Cl3…H6, 3.91 Å) of
the o-amino-benzophenone ring. Moreover, in the case of 2b, there
is an extra interaction between the benzyl m-Cl and the o-hydrogen
(Cl3…H24, 3.43 Å) of the benzophenone phenyl group. The deviation
from the ideal (0o) parallelity of the o-amino-benzophenone and
Structures of Ala Schiff base Ni(II) complexes 2a-2h
Similar to the discussion of Gly complexes, we selected Ala
complexes (S)(2S)-2a16g and (S)(2S)-2b,17a derived from
unsubstituted (S)-4a and tri-chloro-containing ligand (S)-4b,
respectively. Quite unexpectedly, in sharp contrast to Gly complex
1a, in the crystallographic structure of Ala complex 2a (Figure 5),
the benzyl group is clearly engaged in aromatic interactions21,23 with
benzophenone o-amino-phenyl similarly to that observed in the
structure of tri-chloro-Gly complex 1b. Thus, the distances between
nearest C/H atoms are 3.35-3.86 Å (C19…H20, 3.58 Å; C20…H8, 3.35
4 | J. Name., 2012, 00, 1-3
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benzyl rings in Ala complexes 2a and 2b was estimated24 as 14.34o
and 7.33o, respectively.
As discussed above, the arrangement of the chelate rings in
complexes 2a and 2b has the same down-up-down pattern;
however, the N-Ni-O and the N-Ni-N bonding in 2b is more
markedly bent showing angles of 175.61o and 177.47o, respectively
(Figure 6).
Fig. 8 Dihedral angles of the Ala containing chelate rings in
complexes 2a and 2b.
As a result of these differences in the bending of the Ala containing
chelate rings, the methyl groups in complexes 2a and 2b have
different steric environment. Thus, as shown in the Figure 9, the
distance between the CH hydrogen atom and the o-carbon of the
benzophenone ring is 2.64 Å and between the methyl and another
o-carbon is 2.83 Å. By contrast, in Ala 2b complex, these distances
are noticeably greater, measuring 2.77 Å and 3.10 Å, respectively.
Fig. 6 Deviation from planarity of the Ni(II) coordination sphere in
Ala complexes 2a and 2b.
Even more profound difference is observed in the degree of
puckering, which can be estimated by the dihedral angles presented
in Figure 7.
Fig. 9 The distance between the CH hydrogen atom and the o-
carbon of the benzophenone ring in complexes 2a and 2b.
Fig. 7 Dihedral angles of Ni(II) chelate rings in Ala complexes 2a and
2b.
In other words, the methyl group in complex 2a has some steric
repulsive interactions with the benzophenone phenyl ring, while in
complex 2b, the Ala moiety is steric interactions free. Accordingly,
this observation is the first rational and fully credible explanation of
the greater thermodynamic stability of complex 2b over 2a and
therefore, the reported differences in the diastereoselectivity.
The observed trend is also observed in the structures of other Ala
Schiff base complexes (S)(2S)-2 (Scheme 1). For example, Figure 10
presents the structure of the Ala Schiff base complex 2c, derived
from the corresponding p-fluoro-benzyl containing ligand.
Most likely, the higher degree of parallelity between the o-amino-
benzophenone and benzyl rings in 2b, induces the greater twisting
of the chelate rings. Of particular interest is the geometry of the Ala
moiety containing chelate rings presented in Figure 8. One might
agree, that the difference between 2a and 2b is quite significant,
with the methyl group, in the latter, is pointing down almost
perpendicularly relatively the Ala chelate ring.
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Fig. 10 Structure of the Ala Schiff base complex 2c.
Fig. 11 Crystallographic structure of complex (S)(2S)-5 containing
residue of (S)-t-leucine.
Measurement of our key parameters such as the parallelity (C/H Ar-
Ar 3.53-3.80 Å) of the benzyl and the o-amino-phenyl and the
distance between the phenyl o-carbon and the methyl group, gives
the values of 12.56o and 3.00 Å, respectively.
Similar high degree of parallelity (11.52o) is also found in the
crystallographic structure of complex (R)(2R)-6 (Figure 12), derived
from (R)-tryptophan and (R)-configured tri-chloro-ligand 4b.17b
Critical examination of the crystallographic structures of a series of
other Ala complexes 2d-2h gave the data presented in Table 1.
Table 1 Parallelity of the benzyl and the o-amino-phenyl and the
distance between the phenyl o-carbon and the methyl group in Ala
Schiff base complexes 2d-2h
No.
2d
2e
2f
parallelity (o)
distance (Å)
2.97
11.26
Fig. 12 Crystallographic structure of complex (R)(2R)-6 containing
residue of (R)-tryptophan.
15.43
2.69
15.31
2.74
2g
2h
16.43
2.89
The examples of complexes (S)(2S)-5 and (R)(2R)-6, representing
examples of tailor-made, extremely bulky and aromatic amino acids,
undoubtedly underscore the generality of the discovered structural
facets allowing elucidation and prediction of the degree of
diastereomeric preferences based on structural features.
30.49
2.74
As one can see from these data, the higher parallelity of the benzyl
and the o-amino-phenyl is generally reflected by the greater
distance between the phenyl o-carbon and the methyl group. Based
on this trend, we can confidently predict that Ala complexes 2b-2d
are more thermodynamically stable as compared with that of the
parent unsubstituted complex 2a. On the other hand, derivatives
2e-2h will show a similar to 2a, or worse diastereoselectivity.
Very importantly, the discovered trend holds true also for the
complexes containing other than Ala residues. For example,
according to the crystallographic structure of complex (S)(2S)-517a
(Figure 11), containing residue of (S)-t-leucine, the di-chloro-benzyl
and the benzophenone chloro-phenyl rings show nearly perfect
parallel displaced aromatic interactions with deviation from ideal
parallelity of only 6.15o.25
Finally, to complete this study, we would like to emphasize that the
type of aromatic stacking interactions found in the major (S)(2S)-2,
(S)(2S)-5 or (R)(2R)-6 diastereomers, cannot be attained in the case
of the corresponding minor (S)(2R)-3 or (R)(2S)-3 configured
products. As shown in Figure 13, the Ala methyl group, pointing up,
pushes the benzyl group away, preventing its interactions with the
benzophenone aromatic ring. Correspondingly, these (S)(2R)-3 or
(R)(2S)-3 diastereomers are lacking stabilization effect of the
aromatic interactions and, under the conditions of thermodynamic
equilibration will be epimerized to the major products of favorable
(S)(2S)-3 or (R)(2R)-3 absolute configuration.
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1
2
For definition of tailor-made amino acids, see: V. A.
Soloshonok, C. Cai, V. J. Hruby, V. J. Meervelt and N.
Mischenko, Tetrahedron, 1999, 55, 12031.
(a) J. S. Ma, Chim. Oggi, 2003, 21, 65; (b) D. R. W. Hodgson
and J. M. Sanderson, Chem. Soc. Rev., 2004, 33, 422; (c) T.
Sato, K. Izawa, J. L. Aceña and H. Liu, V. A. Soloshonok, Eur. J.
Org. Chem., 2016, 2757.
Fig. 13 Crystallographic structure of the minor diastereomer (S)(2R)-
3b.
3
For recent reviews, see: (a) H. Vogt and S. Brase, Org.
Biomol. Chem., 2007,
Sorochinsky and V. A. Soloshonok, Future Med. Chem., 2009,
, 793; (c) J. L. Aceña, A. E. Sorochinsky and V. A. Soloshonok,
Synthesis, 2012, 1591; (d) K. Bera and I. N. N. Namboothiri,
Asian J. Org. Chem., 2014, , 1234; (e) A. E. Metz and M. C.
5, 406; (b) V. P. Kukhar, A. E.
1
Conclusions
The performed critical analysis of the crystallographic structures of
13 amino acid Schiff base Ni(II) complexes allowed the deduction of
some common underlying structural features. Among which, the
aromatic stacking, parallel displaced type of interactions between
the o-amino-benzophenone and the Pro N-benzyl rings, were found
of primary importance in shaping up the spatial arrangements of
these Ni(II) complexes. The quality of these aromatic interactions
can be evaluated using the degree of parallelity of the interacting
aromatic rings. One of the synthetically important consequences of
the aromatic interactions is the steric environment around the
amino acid side-chain, rendering variously substituted Ni(II)
complexes of different thermodynamic stability. The discovered
structural trend holds true for aliphatic, aromatic and sterically
bulky amino acids and can be used for the rational design of new
and more efficient chiral ligands for general asymmetric synthesis
of tailor-made α-amino acids.
3
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Acknowledgements
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The research leading to these results has received fundings from
the National Natural Science Foundation of China (21632008,
81620108207, and 9122904), the Major Project of Chinese National
Programs for Fundamental Research and Development
(2015CB910304), National S&T Major Projects (2014ZX09507002-
001), and the IKERBASQUE, Basque Foundation for Science (V. A. S.).
E. Schwieter and J. N. Johnston, Chem. Sci. 2015,
6, 2590; (f)
M. Hutchby, A. C. Sedgwick, S. D. Bull, Synthesis, 2016, 48
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and J. A. Ellman, J. Org. Chem., 2016, 81, 1547; (h) R.
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Notes and references
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to estimate the degree of parallelity of the o-amino-
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J. Name., 2013, 00, 1-3 | 9
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ARTICLE
Chem. A., 2006, 110, 10656; (c) E. C. Lee , B. H. Hong , J. Y.
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Table of Contents
Analysis of crystallographic structures of Ni(II) complexes of αꢀamino acid Schiff
bases; Elucidation of the substituents effect on stereochemical preferences
This work disclosed the significance of parallel displaced type of aromatic
interactions between o-amino-benzophenone and N-benzyl rings in Ni(II) complexes.