Different substituent effects on the supramolecular arrays in some (E)-halo- and nitro-benzaldehyde oximes: Confirmation of attractive π(C=N)···π(phenyl) interactions

Article abstract of DOI:10.1515/znb-2018-0222

The crystal structures and Hirshfeld surface analyses are reported for four aldoximes, (E)-X-C₆ H₄ CH=N-OH [X = 3-Cl (1), 4-F (2), 2-O₂ N (3) and 4-O₂ N (4)]. The strong classical O-H · · · N hydrogen bonds involving the oxime group generate C(3) chains in compound 1, in contrast to the R²₂ (6) dimers formed in compounds 2-4; such arrangements have been shown to be the most frequently found for oximes other than salicylaldoximes (2-hydroxybenzaldehyde oximes). In general, weaker intermolecular interactions involving the X substituents, as well as C-H · · · O and π · · · π interactions have significant effects on the supramolecular arrays generated in the aggegation. A further important interaction in compound 1, and to a lesser extent in compound 4, is a π(C=N) · · · π(phenyl) molecular stacking. A data base search has indicated that short Cg(C=N) · · · Cg(phenyl) distances, <3.3 ? (Cg = centre of gravity), have been found in various compounds, including other oximes. A theoretical study was carried out starting from the crystal structure data of compound 1, with optimisation at the BLYP-D3/def2-DZVP level, as well as at the higher PBE0/ma-def2-TZVP level. Breakdown of the interaction energy into separate contributions was achieved using SAPT (using the jun-cc-pvdz basis set). Overall, the calculations indicate that the π(C=N) ·· · π(phenyl) interaction is attractive, with a magnitude of 14-18 kJ mol^-1.

Full text of DOI:10.1515/znb-2018-0222

Z. Naturforsch. 2019; 74(4)b: 319–334
Ligia R. Gomes, John N. Low*, Tanja van Mourik, Herbert Früchtl, Marcus V.N. de Souza,
CDriisftfieanreeFn. tdasCuobstsataintduJeanmteseLf.fWeacrtdsello*n the supramolecular arrays in
some (E)-halo- and nitro-benzaldehyde oximes: confirmation of
attractive π(C=N)ꢀ·ꢀ·ꢀ·ꢀπ(phenyl) interactions
https://doi.org/10.1515/znb-2018-0222
of the interaction energy into separate contributions
was achieved using SAPT (using the jun-cc-pvdz basis
set). Overall, the calculations indicate that the π(C=N)
·ꢀ·ꢀ·ꢀπ(phenyl) interaction is attractive, with a magnitude of
14–18 kJ mol−1.
Received October 5, 2018; accepted February 20, 2019
Abstract: The crystal structures and Hirshfeld surface anal-
yses are reported for four aldoximes, (E)-X–C6H4CH=N–OH
[Xꢀ=ꢀ3-Cl (1), 4-F (2), 2-O2N (3) and 4-O2N (4)]. The strong
classical O–Hꢀ·ꢀ·ꢀ·ꢀN hydrogen bonds involving the oxime Keywords: π(C=N)ꢀ·ꢀ·ꢀ·ꢀπ(phenyl) interactions; aldoximes;
group generate C(3) chains in compound 1, in contrast crystal structures; quantum chemical calculations.
to the R22(6) dimers formed in compounds 2–4; such
arrangements have been shown to be the most frequently
found for oximes other than salicylaldoximes (2-hydroxy-
benzaldehyde oximes). In general, weaker intermolecu- 1 Introduction
lar interactions involving the X substituents, as well as
C–Hꢀ·ꢀ·ꢀ·ꢀO and πꢀ·ꢀ·ꢀ·ꢀπ interactions have significant effects The oxime group, R1R2C=NOH, is found in many biologi-
on the supramolecular arrays generated in the aggega- cally active compounds [1, 2], with a wide range of uses
tion. A further important interaction in compound 1, and including as antitumor agents [3–6], acaricides and
to a lesser extent in compound 4, is a π(C=N)ꢀ·ꢀ·ꢀ·ꢀπ(phenyl) insecticides [7], thymidine phosphorylase inhibitors
molecular stacking. A data base search has indicated that [8], anti-microbial agents [9], bactericides [10] and anti-
short Cg(C=N)ꢀ·ꢀ·ꢀ·ꢀCg(phenyl) distances, <3.3 Å (Cgꢀ=ꢀcen- inflammatory agents [11], as well as in the treatment of
tre of gravity), have been found in various compounds, nerve-gas poisoning [12–15]. In the plant kingdom, oximes
including other oximes. A theoretical study was carried play vital metabolic roles [16]. As an important group of
out starting from the crystal structure data of compound 1, organic compounds, it is not surprising that crystal struc-
with optimisation at the BLYP-D3/def2-DZVP level, as well tures of aldoximes have attracted attention [16–19], with
as at the higher PBE0/ma-def2-TZVP level. Breakdown well over 60 structures listed in the CCDC data base.
Benzaldehyde oximes, ArCH=NOH, with their
-CH=N–OH functional group are ideally arranged for
classical O–Hꢀ·ꢀ·ꢀ·ꢀO and/ or O–Hꢀ·ꢀ·ꢀ·ꢀN hydrogen bonding.
*Corresponding authors: John N. Low, Department of Chemistry,
The last survey of the classical hydrogen bonding pat-
University of Aberdeen, Meston Walk, Old Aberdeen, AB24 3UE,
terns in benzaldehyde oximes reported in 2010 [19] con-
Scotland, UK, e-mail: jnl111@gmail.com; and James L. Wardell,
firmed the most frequently found arrangements, with
Department of Chemistry, University of Aberdeen, Meston Walk, Old
Aberdeen, AB24 3UE, Scotland, UK; and Instituto de Tecnologia em
the exception of salicylaldoxines, were R22 (6) dimers
Fármacos e Farmanguinhos, Fundação Oswaldo Cruz, 21041-250 Rio
de Janeiro, RJ, Brazil, e-mail: j.wardell@abdn.ac.uk
Ligia R. Gomes: FP-ENAS-Faculdade de Ciências de Saúde, Escola
Superior de Saúde da UFP, Universidade Fernando Pessoa,
Rua Carlos da Maia, 296, P-4200-150 Porto, Portugal; and
REQUIMTE, Departamento de Química e Bioquímica, Faculdade de
Ciências da, Universidade do Porto, Rua do Campo Alegre, 687,
P-4169-007 Porto, Portugal
Tanja van Mourik and Herbert Früchtl: School of Chemistry,
University of St. Andrews, North Haugh, St. Andrews, Fife KY16 9ST,
Scotland, UK
Marcus V.N. de Souza and Cristiane F. da Costa: Instituto de
Tecnologia em Fármacos e Farmanguinhos, Fundação Oswaldo Cruz,
21041-250 Rio de Janeiro, RJ, Brazil
and C(3) chains, Fig. 1. Aakerby et al. in 2013 reported
the percentages of R22 (6) dimers and C(3) chains found
in non-salicylaldoxine to be ca.72 and 24%, respectively
[20], and similar percentages can be concluded from
the most recent survey carried out on June 1st, 2018. The
remaining percentage is taken up mainly by compounds
in which the oxime group preferentially interacts with
an acceptor substituent in the aryl unit, for example as
found in pyridinyl compounds [20]. However for other
heteroaromatic aldoximes (furanyl, thienyl and pyrro-
lyl derivatives), as we recently reported, C(3) chains are
formed [21].
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ꢀꢀꢀꢁ
320ꢁ
ꢁL.R. Gomes et al.: Different substituent effects on the supramolecular arrays
C
N
H
O
H
H
O
H
H
N
C
C
N
N
C
H
H
O
H
O
C
N
H
O
H
R 22 (6) dimer
C3 chain
Fig. 1:ꢀIllustrations of the C3 chains and R22(6) dimers formed by oximes.
Hydrogen bonds are considered as the strongest and interactions derived specifically from halo and nitro
most directional of intermolecular interactions available substituents.
in molecules [22] and thus play the major role in determin-
ing the overall supramolecular structures. However, the
involvement of weaker intermolecular interactions, such
2 Results and Discussion
as C–Hꢀ·ꢀ·ꢀ·ꢀO hydrogen bonds, πꢀ·ꢀ·ꢀ·ꢀπ interactions and
interactions involving the substituents can have a signifi-
cant influence on the supramolecular arrays generated in 2.1 General
the aggregation.
In a further study of benzaldehyde oximes, we have The asymmetric unit of each compound, 1–4, contains
determined the crystal structures of four compounds, a single molecule. All four compounds crystallize in the
namely 3-chlorobenzaldehyde oxime, 1, 4-fluorobenza- monoclinic system: compounds 1, 2 and 4 in space group
ldehyde oxime, 2, 2-nitrobenzaldehyde oxime, 3, and P21/c and compound 3 in P21/n, all with Zꢀ=ꢀ4. The geom-
4-nitrobenzaldehyde oxime, 4, from data collected at etry around the oxime moieties is (E) in all four molecules.
Tꢀ=ꢀ100 K, see Scheme 1. The crystal structure of 4 has Figure 2 illustrates the atom arrangements and number-
previously been determined from data collected at room ing schemes. The interplanar angles between the sub-
temperature, and the same P21/c phase was found in each stituents and their attached phenyl group are all less than
case [23–25]. These earlier studies made no mention of 10° in compounds 1, 2 and 4, but in the ortho-substituted
the intermolecular interactions, aside from the classical compound, 3, all such angles are greater than 26°, due
hydrogen bonds involving the oxime atoms. Aims of this to steric hindrance between the nitro and oxime groups
R2 (6)
study were to further investigate the occurrence of
(Table 1). Details of the hydrogen bonding and other
2
dimers and C(3) chains in non-salicylaldoxime deriva- intermolecular interactions are provided in Table 2. The
tives, the importance of π(C=N)ꢀ·ꢀ·ꢀ·ꢀπ(phenyl) interac- major intermolecular interactions in 1–4 involve the
tions in benzaldehyde oxime derivatives in general, O13–H13ꢀ·ꢀ·ꢀ·ꢀN12 hydrogen bonds. In 1 these generate
and the influence of other weaker intermolecular C(3) chains which run parallel to the b axis formed by
X
X
1: X = 3-Cl
2: X = 4-F
3: X = 2-O2N
4: X = 4-O2N
H2NNOH, HCl
K2CO3
C
O
C
N
H
O
H
H
Scheme 1:ꢀSynthesis of 1–4.
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ꢁꢀꢀꢀ
L.R. Gomes et al.: Different substituent effects on the supramolecular arraysꢂ
ꢂ321
1
2
3
4
Fig. 2:ꢀViews of the asymmetric units of 1–4 with the atom numbering schemes. Displacement ellipsoids are drawn at the 80% probability
level, hydrogen atoms as spheres with arbitrary radii.
the action of the screw axis at (1/2, y, 1/4) (Fig. 3), whilst
Table 1:ꢀInterplanar angles (deg) for compounds 1–4.
R2 (6)
in 2–4, the O13–H13ꢀ·ꢀ·ꢀ·ꢀN12 hydrogen bonds form
2
ꢂ
Between oximeꢂ
group and attached
phenyl ring
Between nitroꢂ
group and attached
phenyl ring
Between
oxime and
dimers across the centres of symmetry at (1/2, 0, 1/2), (1,
R2 (6)
̅
1/2, 1/2) and (1, 1, 1), respectively. Within the
dimers
2
nitro groups
of compounds 2–4 there are O13–H13ꢀ·ꢀ·ꢀ·ꢀO13 hydrogen
bonds, with longer than usual H13ꢀ·ꢀ·ꢀ·ꢀO13 distances, of
2.585(19), 2.636(18) and 2.59(2) Å, respectively, and small
O13–H13ꢀ·ꢀ·ꢀ·ꢀO13 angles, near 120°, see (Table 2). The
involvement of pairs of the O13–H13ꢀ·ꢀ·ꢀ·ꢀO13 hydrogen
1ꢃ
2ꢃ
3ꢃ
4ꢃ
7.60(1)ꢃ
9.63(1)ꢃ
37.82(1)ꢃ
8.25(1)ꢃ
ꢃ
ꢃ
26.2(1)ꢃ
3.86(1)ꢃ
39.26(1)
4.86(1)
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322ꢁ ꢁL.R. Gomes et al.: Different substituent effects on the supramolecular arrays
Table 2:ꢀGeometric parameters and symmetry operations for hydrogen bonds and intermolecular interactions (Å, deg).a
Intermolecular hydrogen bonds
ꢂ
D–Hꢀ·ꢀ·ꢀ·ꢀA
ꢂ
D–Hꢂ
Hꢀ·ꢀ·ꢀ·ꢀAꢂ
Dꢀ·ꢀ·ꢀ·ꢀAꢂ
D–Hꢀ·ꢀ·ꢀ·ꢀAꢂ
Symmetry code
1ꢃ
2ꢃ
2ꢃ
2ꢃ
2ꢃ
2ꢃ
3ꢃ
3ꢃ
3ꢃ
3ꢃ
4ꢃ
4ꢃ
4ꢃ
4ꢃ
O13–H13ꢁ·ꢁ·ꢁ·ꢁN12
O13–H13ꢁ·ꢁ·ꢁ·ꢁO13
O13–H13ꢁ·ꢁ·ꢁ·ꢁN12
C3–H3ꢁ·ꢁ·ꢁ·ꢁF4
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
0.85(3)ꢃ
1.00(2)ꢃ
1.00(2)ꢃ
0.95ꢃ
1.96(3)ꢃ
2.585(19)ꢃ
1.88(2)ꢃ
2.58ꢃ
2.8007(18)ꢃ
3.2002(10)ꢃ
2.7991(11)ꢃ
3.4670(13)ꢃ
3.4416(13)ꢃ
3.4229(13)ꢃ
3.2451(17)ꢃ
2.8016(13)ꢃ
3.3132(15)ꢃ
3.1744(15)ꢃ
3.2559(19)ꢃ
2.8191(15)ꢃ
3.3032(16)ꢃ
3.1577(15)ꢃ
177(3)ꢃ
119.7(13)ꢃ
151.8(16)ꢃ
156ꢃ
–xꢁ+ꢁ1, yꢁ+ꢁ1/2, –zꢁ+ꢁ1/2
–xꢁ+ꢁ1, –y, –zꢁ+ꢁ1
–xꢁ+ꢁ1, –y, –zꢁ+ꢁ1
–x, y–1/2, –zꢁ+ꢁ1/2
–x, –y, –z
C5–H5ꢁ·ꢁ·ꢁ·ꢁF4
0.95ꢃ
2.65ꢃ
142ꢃ
C11–H11ꢁ·ꢁ·ꢁ·ꢁO13
O13–H13ꢁ·ꢁ·ꢁ·ꢁO13
O13–H13ꢁ·ꢁ·ꢁ·ꢁN12
C3–H3ꢁ·ꢁ·ꢁ·ꢁO13
0.95ꢃ
2.50ꢃ
165ꢃ
–xꢁ+ꢁ1, yꢁ+ꢁ1/2, –zꢁ+ꢁ1/2
–xꢁ+ꢁ2, –yꢁ+ꢁ1, –zꢁ+ꢁ1
–xꢁ+ꢁ2, –yꢁ+ꢁ1, –zꢁ+ꢁ1
–xꢁ+ꢁ3/2, y–1/2, –zꢁ+ꢁ1/2
–x–3/2, y–1/2, –z–3/2
–xꢁ+ꢁ1, –yꢁ–ꢁ1, –zꢁ+ꢁ1
–xꢁ+ꢁ1, –yꢁ–ꢁ1, –zꢁ+ꢁ1
xꢁ+ꢁ1, yꢁ–ꢁ1, z
0.921(19)ꢃ
0.921(19)ꢃ
0.95ꢃ
2.636(18)ꢃ
1.937(19)ꢃ
2.47ꢃ
124.3(13)ꢃ
155.5(15)ꢃ
148ꢃ
C6–H6ꢁ·ꢁ·ꢁ·ꢁO23
0.95ꢃ
2.60ꢃ
119ꢃ
O13—H13ꢁ·ꢁ·ꢁ·ꢁO13
O13—H13ꢁ·ꢁ·ꢁ·ꢁN12
C6—H6ꢁ·ꢁ·ꢁ·ꢁO41
C11—H11ꢁ·ꢁ·ꢁ·ꢁO41
0.89 (1)ꢃ
0.89 (1)ꢃ
0.95ꢃ
2.68 (2)ꢃ
1.99 (1)ꢃ
2.53ꢃ
124 (2)ꢃ
154(2)ꢃ
139ꢃ
0.95ꢃ
2.42ꢃ
134ꢃ
xꢁ+ꢁ1, yꢁ–ꢁ1, z
Y–Xꢀ·ꢀ·ꢀ·ꢀπ interactions
ꢂ
Y–Xꢀ·ꢀ·ꢀ·ꢀCg
ꢂ
Xꢀ·ꢀ·ꢀ·ꢀCg
ꢂ
Xperp
ꢂ
γ
ꢂ Y–Xꢀ·ꢀ·ꢀ·ꢀCg
ꢂ
Yꢀ·ꢀ·ꢀ·ꢀCgꢂ
Symmetry code
4ꢃ
4ꢃ
N41–O41ꢁ·ꢁ·ꢁ·ꢁCg1 ꢃ
N42–O41ꢁ·ꢁ·ꢁ·ꢁCg1 ꢃ
3.8471(10)
3.3858(10)
ꢃ 3.480
ꢃ 3.345
ꢃ 25.25
ꢃ
ꢃ
65.05(6)
85.57(7)
ꢃ 3.5105(11)(15)ꢃ
x, 1ꢁ+ꢁy, z
x, 1ꢁ+ꢁy, z
ꢃ
8.89
ꢃ
3.5105(11)ꢃ
πꢀ·ꢀ·ꢀ·ꢀπ interactionsa
CgIꢀ·ꢀ·ꢀ·ꢀCg(J)
Cgꢀ·ꢀ·ꢀ·ꢀCg
α
β
γ
CgIperp
CgJperp
Slippage
Symmetry code
2
2
3
3
Cgꢁ·ꢁ·ꢁ·ꢁCg
Cgꢁ·ꢁ·ꢁ·ꢁCg
Cgꢁ·ꢁ·ꢁ·ꢁCg
Cgꢁ·ꢁ·ꢁ·ꢁCg
3.7672(7)
3.7672(7)
3.6405(7)
3.6405(7)
0
0
0
0
24.8
24.8
24.8
15.6
15.6
3.4186(5)
3.4186(5)
3.5064(4)
3.5063(4)
3.4186(5)
3.4185(5)
3.5063(4)
3.5064(4)
1.583
1.583
0.979
0.979
x, –1ꢁ+ꢁy, z
x, 1ꢁ+ꢁy, z
–1ꢁ+ꢁx, y, z
1ꢁ+ꢁx, y, z
24.8
15.6
15.6
aαꢁ=ꢁDihedral angle between planes I and J (deg); βꢁ=ꢁangle Cg(I)→Cg(J); γꢁ=ꢁangle Cg(I)→Cg(J) vector and normal to plane J (deg); Cgꢁ·ꢁ·ꢁ·ꢁCgꢁ=ꢁdistance
between ring centroids (Å); CgIPerpꢁ=ꢁperpendicular distance of Cg(I) on ring J (Å); CgJperpꢁ=ꢁperpendicular distance of Cg(J) on ring I (Å).
R22 (6)
bonds subdivides the
R2 (3)
dimers into three rings –
R2 (4)
R2 (3)
two
rings and one
ring. Such
and cen-
1
2
1
R2 (4)
trosymmetric
rings have been variously reported for
2
organic molecules. Indeed a recent CCDC data base search
revealed more than 500 entries of non-solvated structures
having centrosymmetric H2O2 rings with H–O–H angles
of 120° or less and H–O distances up to the sum of the
contact radii, 2.72 Å, of oxygen and hydrogen. In particu-
lar, the literature search indicated that various aldoxi-
R2 (6)
mes, but not all, possess similar sub-divided
rings,
2
with much smaller H–O distances, e.g., less than 2.60 Å:
examples include 4-Me2NC6H4CH=NOH from room tem-
perature data [CCDC codes MABZOX and 1208893: ref 26]
and more from data at low temperatures [e.g. 2,3-Me2-4-
MeOC6H2CH=NOH: CCDC codes OKUHAD and 161452; ref
27]: 4-BrC6H4CH=NOH: CCDC codes BAGWOW and 181389:
ref 28]. The data for compounds 2–4 are thus not unusual
and do suggest that the O13–H13ꢀ·ꢀ·ꢀ·ꢀO13 hydrogen bonds
can be considered as contributing to the overall stability of
Fig. 3:ꢀThe C3 chain in compound 1, formed from C13–H13ꢁ·ꢁ·ꢁ·ꢁN12
hydrogen bonds. Table 3 lists the symmetry operations.
R2 (6)
R2 (6)
the
dimers. Two views of each of the
dimers are
2
2
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ꢁꢀꢀꢀ
L.R. Gomes et al.: Different substituent effects on the supramolecular arraysꢂ
ꢂ323
2
3
4
Fig. 4:ꢀTwo views of the R22(6) dimers for compounds 2, 3 and 4.
shown in Fig. 4, one looking face-on and the other side-on intermolecular contacts, which link the C3 chains: the
to the parallel phenyl rings. The perpendicular distances Clꢀ·ꢀ·ꢀ·ꢀCl distance is 3.418(6) Å, just within the sum of
R2 (6)
between the parallel phenyl rings in the
dimers are the contact radii of 3.50 Å (symmetry code: iꢀ=ꢀ–x, –y,
2
0.955, 2.609 and 0.751 Å, respectively in 2–4 (Fig. 4): the –z), and (ii) π(C=N)ꢀ·ꢀ·ꢀ·ꢀπ(phenyl) interactions, with a
greater distance in compound 3 reflects the greater devia- Cg(C=N)ꢀ·ꢀ·ꢀ·ꢀCg(phenyl)ii distance of 3.290(1) Å (Cg being
tion of its oxime unit from the plane of its attached phenyl the center of gravity of the phenyl ring): symmetry code:
group as a consequence of steric hindrance between its iiꢀ=ꢀx, −1ꢀ+ꢀy, z) (Fig. 5). The π(C=N)ꢀ·ꢀ·ꢀ·ꢀπ(phenyl) interaction
groups in ortho-position.
is more fully discussed in the Section: π(C=N)ꢀ·ꢀ·ꢀ·ꢀπ(phenyl)
Table 3 lists the percentage atom-atom contacts for all contacts below.
compounds.
The Hirshfeld surface and Fingerprint (FP) plots
[29, 30] for compound 1 are shown in Fig. 6. The Cꢀ·ꢀ·ꢀ·ꢀC,
Clꢀ·ꢀ·ꢀ·ꢀCl and Nꢀ·ꢀ·ꢀ·ꢀH close contacts are designated as are
the site of the πꢀ·ꢀ·ꢀ·ꢀπ contacts. In the FP plot, the two spikes
pointing southwest relate to Nꢀ·ꢀ·ꢀ·ꢀH contacts including
those making the C(3) chains; the high density of pixels
near diꢀ≈ꢀdeꢀ≈ꢀ1.8 Å is due to Cꢀ·ꢀ·ꢀ·ꢀC contacts, and that close
to the diꢀ≈ꢀdeꢀ≈ꢀ1.8–2.0 Å region is due to Clꢀ·ꢀ·ꢀ·ꢀCl contacts,
2.2 Other intermolecular interactions in
individual compounds
2.2.1 The chain-forming compound 1
Interactions in 1, in addition to the C(3) chain forming and the wings ending approximately at (di; de)ꢀ≈ꢀ(1.2; 1.8) Å
O13–H13ꢀ·ꢀ·ꢀ·ꢀN12 hydrogen bond, are (i) short Clꢀ·ꢀ·ꢀ·ꢀCli are due to Hꢀ·ꢀ·ꢀ·ꢀCl contacts.
Table 3:ꢀPercentages of atom-atom contacts.
Compound Hꢀ·ꢀ·ꢀ·ꢀH Hꢀ·ꢀ·ꢀ·ꢀO/Oꢀ·ꢀ·ꢀ·ꢀH Hꢀ·ꢀ·ꢀ·ꢀC/Cꢀ·ꢀ·ꢀ·ꢀH Hꢀ·ꢀ·ꢀ·ꢀN/Nꢀ·ꢀ·ꢀ·ꢀH Cꢀ·ꢀ·ꢀ·ꢀC Oꢀ·ꢀ·ꢀ·ꢀC/Cꢀ·ꢀ·ꢀ·ꢀO Nꢀ·ꢀ·ꢀ·ꢀO/Oꢀ·ꢀ·ꢀ·ꢀN Nꢀ·ꢀ·ꢀ·ꢀC/Cꢀ·ꢀ·ꢀ·ꢀN Oꢀ·ꢀ·ꢀ·ꢀO
1
2
3
4
26.3
32.0
27.5
29.7
10.5
11.3
38.2
29.1
16.1
13.4
4.7
8.0
10.3
7.5
5.2
9.1
10.8
4.0
2.3
1.0
2.0
9.1
–
0.7
2.8
2.4
2.6
2.9
5.2
3.4
5.1
7.5
7.5
Compound
Hꢀ·ꢀ·ꢀ·ꢀCl/Clꢀ·ꢀ·ꢀ·ꢀH
Clꢀ·ꢀ·ꢀ·ꢀC/Cꢀ·ꢀ·ꢀ·ꢀCl
2.3
Fꢀ·ꢀ·ꢀ·ꢀC/Cꢀ·ꢀ·ꢀ·ꢀF
Fꢀ·ꢀ·ꢀ·ꢀF
Hꢀ·ꢀ·ꢀ·ꢀF/Fꢀ·ꢀ·ꢀ·ꢀH
1
2
24.3
2.1
2.1
17.6
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ꢀꢀꢀꢁ
324ꢁ ꢁL.R. Gomes et al.: Different substituent effects on the supramolecular arrays
(a)
(b)
Fig. 5:ꢀCompound 1. (a) Part of a stack of molecules formed from π(C=N) ··ꢁ·ꢁπ(phenyl) interactions. The Cg(C=N)ꢁ·ꢁ·ꢁ·ꢁCgi (phenyl) distance is
3.290(1) Å (symmetry code: iꢁ=ꢁx, –1ꢁ+ꢁy, z; (b) the overlap of the C=N and phenyl π systems in successive rows of the π(C=N)ꢁ·ꢁ·ꢁ·ꢁπ(phenyl).
(a)
(b)
Fig. 6:ꢀCompound 1. (a) View of the Hirshfeld surface mapped over dnorm: the set of two intense red area spots relate to Nꢁ·ꢁ·ꢁ·ꢁH close contacts
in forming the C3 chain; also designated are the sites of the Cꢁ·ꢁ·ꢁ·ꢁC and πꢁ·ꢁ·ꢁ·ꢁπ contacts; (b) the FP plot, the two spikes pointing southwest
relate to Nꢁ·ꢁ·ꢁ·ꢁH contacts including those making the C(3) chains; the high density of pixels near diꢁ≅ꢁdeꢁ≅ꢁ1.8 Å are due to Cꢁ·ꢁ·ꢁ·ꢁC and those
close to diꢁ≅ꢁdeꢁ≅ꢁ1.8–2.0 Å interval are due to Clꢁ·ꢁ·ꢁ·ꢁCl contacts, wings ending approximately at (di; de)ꢁ≅ꢁ(1.2; 1.8) Å are due to Hꢁ·ꢁ·ꢁ·ꢁCl
contacts.
R2 (8)
Compound
1
has the highest percentage of in Fig. 7a. Within the sheets are
rings, arising from
R2 (6)
2
Hꢀ·ꢀ·ꢀ·ꢀC/Cꢀ·ꢀ·ꢀ·ꢀH contacts and the lowest percentage of the C–Hꢀ·ꢀ·ꢀ·ꢀF hydrogen bonds, as well as the
rings.
Hꢀ·ꢀ·ꢀ·ꢀH and Hꢀ·ꢀ·ꢀ·ꢀO/Oꢀ·ꢀ·ꢀ·ꢀH contacts of all four compounds The overlap of the π systems in successive lay2ers of the
studied here, see Table 3. There is also a high percentage πꢀ·ꢀ·ꢀ·ꢀπ stacks is illustrated in Fig. 7b: the Cgꢀ·ꢀ·ꢀ·ꢀCgi distance
of Hꢀ·ꢀ·ꢀ·ꢀCl/Clꢀ·ꢀ·ꢀ·ꢀH contacts in compound 1.
is 3.7672 (7) Å, and the perpendicular distance between
the planes is 3.4186(5) Å with a slippage of 1.583 Å (sym-
metry code: iꢀ=ꢀx, −1ꢀ+ꢀy, z). The second sub-structure in
compound 2 is a further sheet formed from combinations
of C11–H11ꢀ·ꢀ·ꢀ·ꢀO13 and C3–H3ꢀ·ꢀ·ꢀ·ꢀF4 hydrogen bonds. Each
of these hydrogen bonds individually generates C4 spiral
chains, which run parallel to the b axis, formed by the
2.3 The compounds forming R22(6) dimers
2.3.1 Compound 2
In 2, in addition to the O13–H13ꢀ·ꢀ·ꢀ·ꢀN12 and O13– action of the screw axis at (1/2, y, 1/4). Within this sheet is
R4(22)
H13ꢀ·ꢀ·ꢀ·ꢀO13 hydrogen bonds, there are weaker C11– a network of
rings (Fig. 7c). Combination of the two
4
H11ꢀ·ꢀ·ꢀ·ꢀO13, C3–H3ꢀ·ꢀ·ꢀ·ꢀF4 and C5–H5ꢀ·ꢀ·ꢀ·ꢀF4 hydrogen different sheets generates a three-dimensional array.
bonds, and πꢀ·ꢀ·ꢀ·ꢀπ interactions. The overall structure can
Compound 2 has the highest percentage of Hꢀ·ꢀ·ꢀ·ꢀH
be conveniently considered to be formed from two sub- contacts, 32.0%, significantly higher than the sum,
R22 (6)
structures. Firstly, the
dimers are linked by the 21.8%, of fluorine contacts (Hꢀ·ꢀ·ꢀ·ꢀF/Fꢀ·ꢀ·ꢀ·ꢀH, Fꢀ·ꢀ·ꢀ·ꢀC/Cꢀ·ꢀ·ꢀ·ꢀF
C5–H5ꢀ·ꢀ·ꢀ·ꢀF4 hydrogen bonds into chains, which are further and Fꢀ·ꢀ·ꢀ·ꢀF). The Hꢀ·ꢀ·ꢀ·ꢀO/Oꢀ·ꢀ·ꢀ·ꢀH, Hꢀ·ꢀ·ꢀ·ꢀC/Cꢀ·ꢀ·ꢀ·ꢀH, and
linked by the πꢀ·ꢀ·ꢀ·ꢀπ interactions into sheets, as illustrated Hꢀ·ꢀ·ꢀ·ꢀN/Nꢀ·ꢀ·ꢀ·ꢀH contacts all are ca 10%.
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ꢁꢀꢀꢀ
L.R. Gomes et al.: Different substituent effects on the supramolecular arraysꢂ
ꢂ325
(a)
(b)
(c)
Fig. 7:ꢀCompound 2. (a) Part of a sheet formed from linking the R22(6) dimers with C5–H5ꢁ·ꢁ·ꢁ·ꢁF4 hydrogen bonds and πꢁ·ꢁ·ꢁ·ꢁπ interactions;
(b) the overlap of the π systems in successive layers of the πꢁ·ꢁ·ꢁ·ꢁπ stack, shown in Fig. 7a; (c) part of a sheet formed from linkages using
C11–H11ꢁ·ꢁ·ꢁ·ꢁO13 and C3–H3ꢁ·ꢁ·ꢁ·ꢁF4 hydrogen bonds. Details of the intermolecular interactions are displayed in Table 3.
The three other 4-halobenzaldehyde oximes, (E)-4- and the slippage is 0.979 Å (symmetry code: −1ꢀ+ꢀx, y, z).
XC6H4CH=N–OH (X=Cl [31], Br [28] and I [20]) were also The distance between N21(nitro group) and O22i (nitro
R2 (6)
shown to form
dimers.
group) in successive layers of the stack is 3.0658(13) Å,
which is at the sum of the contact radii and thus does
not suggest any significant nitro group – nitro group
interaction. There is however a short O13(hydroxyl)ꢀ·ꢀ·ꢀ·ꢀO
23ii(nitro) separation of 2.928(13) Å, well within the sum
2
2.3.2 Compound 3
The intermolecular interactions in compound 3, in of the contact radii of 3.04 Å (symmetry code: iiꢀ=ꢀ3/2–x,
addition to the dimer forming O13–H13ꢀ·ꢀ·ꢀ·ꢀN12 and 1/2ꢀ+ꢀy, 1/2–z).
C3–H3ꢀ·ꢀ·ꢀ·ꢀO13 hydrogen bonds, are C6–H6ꢀ·ꢀ·ꢀ·ꢀO23(nitro)
hydrogen bonds and πꢀ·ꢀ·ꢀ·ꢀπ interactions. The R2 (6)
2
dimers are linked by the C3–H3ꢀ·ꢀ·ꢀ·ꢀO13 and 2.3.3 Compound 4
C6–H6ꢀ·ꢀ·ꢀ·ꢀO23 hydrogen bonds into sheets. These sheets
R3(12)
R4(26)
are composed of a network of
and
rings, There are major differences between the contacts found
3
4
R2 (6)
complemented by
rings (Fig. 8a). The sub-structure in compounds 3 and 4, which are both nitro phenyl
2
R2 (6)
generated from linking the
dimers with the πꢀ·ꢀ·ꢀ·ꢀπ derivatives. In compound, 4, in addition to the O13–
2
interactions is illustrated in Fig. 8b. The overlap of the H13ꢀ·ꢀ·ꢀ·ꢀN12 and C3–H3ꢀ·ꢀ·ꢀ·ꢀO13 hydrogen bonds, which
R22 (6)
π systems in successive layers of the stack is shown in form the
dimers, there are other intermolecular
Fig. 8c: the Cgꢀ·ꢀ·ꢀ·ꢀCgi distance is 3.6405(7) Å, the per- interactions solely involving the nitro group atoms.
pendicular distance between the planes is 3.5064 (5)Å Three distinct types of nitro group interactions are found
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ꢀꢀꢀꢁ
326ꢁ
ꢁL.R. Gomes et al.: Different substituent effects on the supramolecular arrays
(a)
(b)
(c)
Fig. 8:ꢀCompound 3. (a) Part of a sheet of molecules formed from combination of O13–H13ꢁ·ꢁ·ꢁ·ꢁN12, C3–H3ꢁ·ꢁ·ꢁ·ꢁO13 and C6–H6ꢁ·ꢁ·ꢁ·ꢁO23 hydrogen
bonds; (b) part of a double πꢁ·ꢁ·ꢁ·ꢁπ stack, formed from the R22(6) dimers; (c) the overlap of the π systems in the stacks shown in Fig. 8b. Details
of the intermolecular interactions are displayed in Table 3.
R2 (6)
in compound 4, all of which link the
dimers into and O42ꢀ·ꢀ·ꢀ·ꢀπiii distances of 3.8471(10) and 3.3858(10)
2
more elaborate sub-structures: (i) the nitro group oxygen Å, respectively (symmetry code iiiꢀ=ꢀx, 1ꢀ+ꢀy, z). The first
atom, O41, acts as the acceptor in C6–H6ꢀ·ꢀ·ꢀ·ꢀO41i and C11– of these interactions, involving the C6–H6ꢀ·ꢀ·ꢀ·ꢀO41 and
H11ꢀ·ꢀ·ꢀ·ꢀO41ii hydrogen bonds (Table 2). (ii) nitroꢀ·ꢀ·ꢀ·ꢀnitro C11–H11ꢀ·ꢀ·ꢀ·ꢀO41 hydrogen bonds, link the R22 (6) dimers
group interactions [32], with a O42ꢀ·ꢀ·ꢀ·ꢀN41iii separation of into tilted two-molecule wide columns as illustrated
R2 (6)
R4(26),
2.8641(13) Å (symmetry code: iiiꢀ=ꢀ–x, 1/2ꢀ+ꢀy, 1/2–z), and in Fig. 9a. Within the columns are
and
as
2
4
R2 (6)
(iii) both the oxygen atoms of the nitro group are used well as
rings. The nitro groups at the ends of the
dimers are involved in the nitroꢀ·ꢀ·ꢀ·ꢀnitro group
2
R22 (6)
in N41–O41ꢀ·ꢀ·ꢀ·ꢀπiii and N41–O42ꢀ·ꢀ·ꢀ·ꢀπiii, with O41ꢀ·ꢀ·ꢀ·ꢀπiii
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ꢁꢀꢀꢀ
L.R. Gomes et al.: Different substituent effects on the supramolecular arraysꢂ
ꢂ327
(a)
(b)
(d)
(e)
(c)
R2 (6)
Fig. 9:ꢀCompound 4. (a) Part of a two-molecular wide tilted sheet formed from linking the
dimers by C6–H6ꢁ·ꢁ·ꢁ·ꢁO41 and
2
C11–H11ꢁ·ꢁ·ꢁ·ꢁO41 hydrogen bonds; (b) the Chevron style arrangement arising from the nitro-nitro group interactions; (c) a part of the
arrangement generated from linking the R22 (6) dimers by N41–O41ꢁ·ꢁ·ꢁ·ꢁπ, N21–O42ꢁ·ꢁ·ꢁ·ꢁπ and the nitro-nitro interaction; (d) part of the stack
obtained from combination of the N41–O41ꢁ·ꢁ·ꢁ·ꢁπ, N21–O42ꢁ·ꢁ·ꢁ·ꢁπ and π (C=N) ··ꢁ·ꢁπ(phenyl) interactions; (e) the overlap of molecules in the
stack shown in Fig. 9d. Details of the intermolecular interactions are displayed in Table 3.
contacts with O41ꢀ·ꢀ·ꢀ·ꢀO42v and O42ꢀ·ꢀ·ꢀ·ꢀN41vi distances in a successive layer, with a Cg(C=N) ·ꢀ·ꢀ·ꢀCg(phenyl) dis-
of 2.9294(11) and 2.8641(13) Å, respectively, both within tance of 3.406 Å, which suggests a π(C=N)ꢀ·ꢀ·ꢀ·ꢀπ(phenyl)
the appropriate sums of the contact radii of 3.04 and 3.07 interaction (Fig. 9d and e). This is longer than the equiva-
Å, respectively (symmetry codes: vꢀ=ꢀ–x, −1/2ꢀ+ꢀy, 1/2–z; lent distance found in compound 1 and, in addition, this
viꢀ=ꢀ–x, 1/2ꢀ+ꢀy, 1/2–z). These nitroꢀ·ꢀ·ꢀ·ꢀnitro group interac- positioning of the C=N unit may be serendipitous and a
tions, which provide a Chevron-type arrangement, are consequence of the other interactions in the column, for
illustrated in Fig. 9b. Figure 9c shows the arrangement example the N41–O41ꢀ·ꢀ·ꢀ·ꢀπ, N41–O42ꢀ·ꢀ·ꢀ·ꢀπ interactions
R2 (6)
obtained from linking the
dimers by N41–O41ꢀ·ꢀ·ꢀ·ꢀπ, (Fig. 9d). However, while it is not so clear cut as the situ-
N41–O42ꢀ·ꢀ·ꢀ·ꢀπ and the nitroꢀ2·ꢀ·ꢀ·ꢀnitro interactions. Within ation in compound 1, such a π(C=N) ·ꢀ·ꢀ·ꢀπ(phenyl) inter-
R2 (6)
this arrangement are layers of
C=N unit of the oxime in one layer sits above a phenyl ring π(C=N) ··ꢀ·ꢀπ(phenyl) interactions.
dimers in which the action is stabilizing as discussed below in the chapter on
2
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328ꢁ ꢁL.R. Gomes et al.: Different substituent effects on the supramolecular arrays
No π(C=N)ꢀ·ꢀ·ꢀ·ꢀπ(phenyl) interaction is apparent in 5,
as the relevant Cgꢀ·ꢀ·ꢀ·ꢀCg distance is >4.4 Å.
2.4 Comparison of the structures of the
three isomeric nitrobenzaldehyde
oximes
Comparisons of the structures of the three isomeric mono- 2.5 Hirshfeld surfaces and FP plots for
nitrobenzaldehyde oximes can be made, as the struc-
ture of 3-nitrobenzaldehyde oxime, 5, has been briefly
compounds, 2–4
reported from data collected at room temperature [33]. Views of the Hirshfeld surface [29, 30] for compounds,
The ortho- and meta-isomers, compounds 3 and 5, have 2–4, which form R22 (6) dimers, are illustrated in Fig. 10.
similar sets of intermolecular interactions, which are For each compound, red areas are designated corre-
significantly different from those of the para-isomer, 4. sponding to O–Hꢀ·ꢀ·ꢀ·ꢀN and Nꢀ·ꢀ·ꢀ·ꢀH–O and other contacts,
R2 (6)
While only the classical hydrogen bonds forming the
including the Oꢀ·ꢀ·ꢀ·ꢀO and Nꢀ·ꢀ·ꢀ·ꢀO close contacts found in
dimers were mentioned in the published report on 4 [233], compound 4. The FP plots for these three compounds are
a deeper analysis of the structure has indicated a strong illustrated in Fig. 11. The similarity of the three FP plots
πꢀ·ꢀ·ꢀ·ꢀπ interaction, with a Cgꢀ·ꢀ·ꢀ·ꢀCg distance of 3.7738(14) is apparent: any differences between the plots arise from
Å, a distance between parallel phenyl rings of 3.4677(10) the different percentages of Hꢀ·ꢀ·ꢀ·ꢀX (X=H, O, N, Cl or F)
Å and a slippage of 1.489 Å, similar to the situation in the contacts for each molecule. The Nꢀ·ꢀ·ꢀ·ꢀH close contacts are
ortho-isomer, 3. Also as in compound 3, the nitro group responsible for the pair of sharp spikes ending at de/di ca
atoms are only involved in C–Hꢀ·ꢀ·ꢀ·ꢀO hydrogen bonds, but 1.2 Å (de and di are the axes of the FP plots). Close to these
rather than the sheet found in compound, 3, only a two- spikes are other, less-sharp, peaks, which correspond to
R2 (6)
molecule wide column is generated from the
dimers Oꢀ·ꢀ·ꢀ·ꢀH contacts, and the area within the spikes appear-
ing as the comb-like teeth is due to Hꢀ·ꢀ·ꢀ·ꢀH close contacts
and the available C–Hꢀ·ꢀ·ꢀ·ꢀO hydrogen bonds in25.
(a)
(b)
(c)
Fig. 10:ꢀViews of the Hirshfeld surface mapped over dnorm for compounds (a) 2, (b) 3 and (c) 4, forming R22(6) rings. In each compound, red
areas relating to O–Hꢁ·ꢁ·ꢁ·ꢁN and Nꢁ·ꢁ·ꢁ·ꢁH–O and other contacts are designated.
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ꢁꢀꢀꢀ
L.R. Gomes et al.: Different substituent effects on the supramolecular arraysꢂ
ꢂ329
(a)
(b)
(c)
Fig. 11:ꢀFP plots for compounds (a) 2, (b) 3 and (c) 4, which form the R22(6) dimers. The Nꢁ·ꢁ·ꢁ·ꢁH close contacts result in the pair of sharp
spikes in the FP plot, ending at de/di ca.1.2 Å. Very close to those spikes are other, less-sharp, peaks which arise from Oꢁ·ꢁ·ꢁ·ꢁH contacts. The
area within the spikes appearing as “teeth of a comb” is due to Hꢁ·ꢁ·ꢁ·ꢁH close contacts involving the H atoms of the hydroxyl group of the
oxime. The higher percentage of Cꢁ·ꢁ·ꢁ·ꢁC contacts in compound 3 are indicated by the higher pixel frequency at de / diꢁ≅ꢁ1.8 Å as shown by the
light green and red areas.
involving the hydroxyl group of the oxime. The small
2.6 π(C=N)ꢀ·ꢀ·ꢀ·ꢀπ(phenyl) interactions
R2 (6)
teeth-like peaks shown in Fig. 11 for the
dimer-form-
2
ing compounds and their absence in the FP plot for the C3 The clear indication of a π(C=N)ꢀ·ꢀ·ꢀ·ꢀπ(phenyl) interaction
chain-forming compound 2, shown in Fig. 6, clearly point in compound 1, and the less clear indication in compound
to major differences in the structures. A breakdown of the 4, led to an investigation of similar interactions in other
Hꢀ·ꢀ·ꢀ·ꢀX (X=H, O, N, and F) contacts in compound 2, is illus- oximes with Cg(C=N)ꢀ·ꢀ·ꢀ·ꢀCg(phenyl) distances up to 3.30
trated in Fig. 12. The percentage atomꢀ·ꢀ·ꢀ·ꢀatom contacts in Å. Among the compounds found were the high pressure
2–4 are shown in Table 3. As expected for the two nitro P21/nphaseofsalicylaldoxime[SALOXM-08][34], thehigh
derivatives, 3 and 4, the combined percentages of close pressure I2/a phase of 3-t-butylsalicylaldoxime [NIRJII-
contacts involving oxygen are high.
07] [35] and benzene-1,3,5-tris(N-hydroxy-methanimine)
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ꢀꢀꢀꢁ
330ꢁ
ꢁL.R. Gomes et al.: Different substituent effects on the supramolecular arrays
(a)
(b)
(c)
(d)
Fig. 12:ꢀPartial FP plots for 2 showing pixels due to (a) Fꢁ·ꢁ·ꢁ·ꢁH, (b) Hꢁ·ꢁ·ꢁ·ꢁH, (c) Nꢁ·ꢁ·ꢁ·ꢁH and (d) Oꢁ·ꢁ·ꢁ·ꢁH contacts.
[ADOJEK][36].Oximeethers,suchas,1-(salicylidene-oxy)- 2.6.1 Theoretical calculations on the potential of
2-(3-methoxysalicylidenesmino-oxy)ethane [FOJROM]
[37] were also found with short Cg(C=N)ꢀ·ꢀ·ꢀ·ꢀCg((phenyl)
π(C=N) ··ꢀ·ꢀπ(phenyl) interactions in compound 1
distances. A search on 12-06-2018 of the CCDC data A theoretical study of the potential π(C=N) ·ꢀ·ꢀ·ꢀπ(phenyl)
base of compounds possessing C=N–X fragments interactions was carried out on compound 1, using ini-
(X=OH, OR, NR1R2 etc) with Cg(C=N)ꢀ·ꢀ·ꢀ·ꢀCg(phenyl) dis- tially a stacked dimer, extracted from the CIF (structure
tances less than 3.30 Å, revealed more than 80 hits. A in Fig. 13). Figure 13 shows the various structures and
Extending the Cg(C=N)ꢀ·ꢀ·ꢀ·ꢀCg(phenyl) distance beyond sub-structures, and their associated calculated interac-
3.30 to 4.0 Å brought in many more compounds. Short tion energies. To separate the two possible intermolecular
Cg(C=N)ꢀ·ꢀ·ꢀ·ꢀCg(phenyl) distances were found to be very interactions in the dimer A – the π(CN)ꢀ·ꢀ·ꢀ·ꢀπ(phenyl) inter-
much less common for compounds with -CH=N–OR (R=H action and the OHꢀ·ꢀ·ꢀ·ꢀN hydrogen bond – two additional
or organyl) fragments, compared to compounds with dimers were constructed: replacement of the CH=N(OH)
C=N–NXY fragments.
moiety by a hydrogen atom in the upper molecule removes
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L.R. Gomes et al.: Different substituent effects on the supramolecular arraysꢂ
ꢂ331
Fig. 13:ꢀStuctures, used in the theoretical calculations on the π(CN)ꢁ·ꢁ·ꢁ·ꢁπ(phenyl) interaction in compound 1, and their energies.
the OHꢀ·ꢀ·ꢀ·ꢀN interaction (structure B) and replacement of In summary, the calculations support that the CNꢀ·ꢀ·ꢀ·ꢀπ
the chlorophenyl unit by a hydrogen atom in both mole- interaction is attractive, with a considerable magnitude
cules removes the potential π(CN) ·ꢀ·ꢀ·ꢀπ(phenyl) interac- estimated to be in the range of −15 to −18 kJ mol−1.
tion (structure C). The interaction energy of structure A
Table 4 shows a breakdown of the interaction energy
(−22.9 kJ mol−1) shows that there is a considerable and into separate contributions using sSAPTO. The sSAPT0
attractive interaction between the two molecules at the interaction energies are in reasonable agreement with the
experimental geometry. However, only part of this attrac- PBE0 values. The results show that dispersion is relatively
tion can be attributed to the π(CN)ꢀ·ꢀ·ꢀ·ꢀπ(phenyl) interac- more important in A and B compared to C, and electrostat-
tion, as there is also an OHꢀ·ꢀ·ꢀ·ꢀN interaction in the dimer. ics are more important in C.
When optimizing the geometry (structure D), this interac-
tion makes the structure less parallel. Structure E, where
one of the molecules is rotated to avoid this OHꢀ·ꢀ·ꢀ·ꢀN inter-
3 Experimental
action, remains parallel and has an interaction energy
of −29.6 kJ mol−1. Assuming that this interaction energy
results from two CNꢀ·ꢀ·ꢀ·ꢀπ interactions, one such interac- 3.1 Synthesis and crystallization
tion is estimated to be −14.8 kJ mol−1.
Structures
B
and
C
aim to eliminate the The compounds, 1–4, were prepared by refluxing the cor-
π(CN)ꢀ·ꢀ·ꢀ·ꢀπ(phenyl) and OHꢀ·ꢀ·ꢀ·ꢀN interactions. The sum of responding aldehyde with hydroxyamine in an aqueous
the interaction energies of B and C (−23.9 kJ mol−1) is not far solution containing potassium carbonate, rather than
off from that of the full dimer (−22.9 kJ mol−1), so it seems pyridine, following a published procedure [45]. They were
reasonable to assume that the interaction energy of the full purified by recrystallization from methanol solutions.
dimer is a sum of the π(CN)ꢀ·ꢀ·ꢀ·ꢀπ(phenyl) and OHꢀ·ꢀ·ꢀ·ꢀN inter-
3-Chlorobenzaldehyde oxime, 1: m.p. 64–65°C [46].
actions. These results suggest that the π(CN)ꢀ·ꢀ·ꢀ·ꢀπ(phenyl) 4-Fluorobenzaldehyde oxime, 2:. m.p. 85–87°C (lit
interaction accounts for −19.3 kJ mol−1. This is a bit higher [http://synquestlabs.com/product/id/53507.html]: m.p.
than the −14.8 kJ mol−1 estimated above, but is probably an 85–86°C). 2-Nitrobenzaldehyde oxime, 3: m.p. 97–98°C
overestimation, as there are more attractive interactions in (lit. [https://www.alfa.com/en/catalog/A14565/]: m.p.
this dimer than just the π(CN)ꢀ·ꢀ·ꢀ·ꢀπ(phenyl) interaction (for 98–102°C). 4-Nitrobenzaldehyde oxime, 4: m.p. 123–124°C
example, with the hydrogen atom of the upper molecule (lit. [https://www.alfa.com/en/catalog/L09144/]: m.p.
above the ring of the lower molecule in structures A and B). 122–125°C).
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332ꢁ ꢁL.R. Gomes et al.: Different substituent effects on the supramolecular arrays
Table 4:ꢀCrystal data.
ꢂ
1
ꢂ
2
ꢂ
3
ꢂ
4
Crystal data
ꢂChemical formula
ꢂMr
ꢂCrystal system, space group
ꢂTemperature, K
ꢂa, b, c, Å
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
C7H6ClNO
155.58
Monoclinic, P21/c
100
12.1214(7),
4.4332(2),
13.6946(8)
109.283(6)
694.62(7)
4
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
C7H6FNO
139.13
Monoclinic, P21/c
100
14.2137(5),
3.7672(1),
11.9364(4)
99.210(3)
630.90(4)
4
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
C7H6N2O3
166.14
Monoclinic, P21/n
100
3.6405(1),
13.4466(6),
14.8993(7)
95.086(4)
726.48(5)
4
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
C7H6N2O3
166.14
Monoclinic, P21/c
100
6.2083(2),
4.8431(2),
24.3013(8)
94.986(3)
727.91(5)
4
ꢂβ, deg
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
ꢂV, Å3
ꢂZ
ꢂRadiation type
MoKα
0.5
0.20ꢁ×ꢁ0.05ꢁ×ꢁ0.03 ꢃ
MoKα
0.1
0.20ꢁ×ꢁ0.10ꢁ×ꢁ0.02 ꢃ
MoKα
0.1
0.15ꢁ×ꢁ0.05ꢁ×ꢁ0.03 ꢃ
MoKα
0.1
0.06ꢁ×ꢁ0.05ꢁ×ꢁ0.01
ꢂμ, mm−1
ꢂCrystal size, mm3
Data collection
ꢂDiffractometer
ꢂAbsorption correction
ꢃ
ꢃ
(a)
(c)
ꢃ
ꢃ
(a)
(c)
ꢃ
ꢃ
(a)
(c)
ꢃ
ꢃ
(b)
(c)
ꢂNo. of measured/independent/ꢃ
14977/1591/1381ꢃ
13530/1443/1349ꢃ
16152/1669/1549ꢃ
8656/1670/1462
observed [Iꢁ>ꢁ2 σ(I)] reflections
ꢂRint
ꢃ
ꢃ
0.068
0.649
ꢃ
ꢃ
0.029
0.649
ꢃ
ꢃ
0.064
0.649
ꢃ
ꢃ
0.021
0.649
ꢂ(sin θ/λ)max, Å–1
Refinement
ꢂNo. of reflections
ꢂNo. of parameters
ꢂNo. of restraints
ꢂH atom treatment
ꢂR[F2ꢁ>ꢁ2 σ(F2)], wR(F2), S
ꢂΔρmax/min, e Å–3
ꢂCCDC No
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
ꢃ
1591
95
0
(d)
0.041, 0.118, 1.08 ꢃ
0.53, –0.37
1846653
ꢃ
ꢃ
ꢃ
ꢃ
1443
95
0
(d)
0.033, 0.101, 1.09 ꢃ
0.35, –0.21
1846654
ꢃ
ꢃ
ꢃ
ꢃ
1669
113
0
ꢃ
ꢃ
ꢃ
ꢃ
1670
113
1
(d)
(d)
0.033, 0.089, 1.07 ꢃ
0.036, 0.102, 1.08
0.38, –0.23
1856711
ꢃ
ꢃ
ꢃ
ꢃ
0.31, –0.16
1846655
ꢃ
ꢃ
(a) Rigaku FREꢁ+ꢁequipped with VHF Varimax confocal mirrors and an AFC12 goniometer and HyPix 6000 detector diffractometer; (b)
XtaLAB AFC12 (RCD3): Kappa single diffractometer; (c) Multi-scan CrysAlis Pro 1.171.39.30d (Rigaku Oxford Diffraction, 2017) Empirical
absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm; (d) H atoms treated by a mixture of
independent and constrained refinement. Computer programs used: CrysAlis PRO 1.171.39.30d [38], Oscail [39], Shelxt [40], ShelXle [41],
Shelxl2017/1 [42], Mercury [43], Platon [44].
all atom positions lie within the maximum contour level.
3.2 Crystallography
All other hydrogen atoms were refined as riding atoms at
Crystal data, data collection and structure refinement a distance of 0.95Å.
details are summarized in Table 5 [38–44]. In each case
The Hirshfeld surfaces and two-dimensional finger-
the oxime group has an (E) geometry. In all compounds print (FP) plots [29, 30] were generated using Crystal
the oxime hydroxyl hydrogen atoms were refined and Explorer 3.1 [29, 30]. The Hirshfeld surface mapped over
their positions checked on a final difference map where
d
norm is scaled in the range −0.68 to 1.17.
Table 5:ꢀBreakdown of the interaction energies of the different
dimers using sSAPT0
3.3 Theoretical study of the
π(C=N)ꢀ·ꢀ·ꢀ·ꢀπ(phenyl) interaction in
compound 1
Structure Electrostatics Exchange Induction Dispersion
Total
A
B
C
D
E
–21.0
–19.7
–2.6
–24.36
–19.07
50.6
50.0
–4.5
–4.5
–50.7 –25.7
–47.3 –21.5 Hydrogen geometries were optimised with the BLYP-D3
4.6
–0.7
–3.8
–45.37 –30.98
–53.27 –32.98
–2.6
density functional (BLYP [47, 48] augmented with
Grimme’s D3 dispersion correction [49] in conjunction
with the def2-SVP basis set [50] using Orca [51], keeping
45.02
43.41
–6.26
–4.05
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ꢁꢀꢀꢀ
L.R. Gomes et al.: Different substituent effects on the supramolecular arraysꢂ
ꢂ333
all other atoms at the experimental geometry. Interaction
energies were computed with PBE0-D3 (the hybrid PBE0
5 Supporting information
functional [52] augmented with D3) and the ma-def2-TZVP CCDC 1846653–1846655 and 1856711 for compounds 1–4,
basis set [50, 53]. The counterpoise procedure [54] was respectively, contain the supplementary crystallographic
used to eliminate BSSE. As the heavy atoms are at the data for this paper. These data can be obtained free of
crystallographic positions, deformation energies were charge from The Cambridge Crystallographic Data Centre
omitted. The interaction energies were thus computed as via www.ccdc.cam.ac.uk/data_request/cif.
follows:
The crystallographic CIFs are also given as supple-
mentary material available online (DOI: 10.1515/znb-2018-
0222).
AB
AB
AB
∆E = EA{ }(AB)– EA{ }(AB)– EA{ }(AB)
(1)
Here, the superscript {AB} denotes that all calculations Acknowledgements: The authors thank the National Crys-
employ the dimer basis set, and the attributes in round tallographic Service, University of Southampton, UK, for
brackets, (AB), denote that all calculations employ the the data collection, and for their help and advice. LRG
dimer geometry.
thanks the Portuguese Foundation for Science and Tech-
Additional calculations at the PBE0-D3/ma-def2- nology (FCT) UID/Multi/04546/2013.for support.
TZVP level employing the counterpoise procedure. The
structures were additionally analyzed with Symmetry-
Adapted Perturbation Theory (SAPT) [55], which calcu-
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4 Conclusions
The crystal structures and the results of the Hirsh-
feld surface analysis of four aldoximes, XC6H4CH=N–OH
(Xꢀ=ꢀ3-Cl (1), 4-F (2), 2-O2N (3) and 4-O2N (4), are reported.
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mol−1.
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Supplementary Material: The online version of this article offers
supplementary material (https://doi.org/10.1515/znb-2018-0222).
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