Synthesis and crystal structures of new phosphoric triamides: study of intermolecular interactions by semi-empirical calculations and Hirshfeld surface analysis

Article abstract of DOI:10.1007/s00706-018-2186-y

Abstract: In the present paper, crystal structures and Hirshfeld surface analyses of two new phosphoric triamides [2,3,6-F₃–C₆H₂C(O)NH]P(O)(X)₂ (X=N(CH₃)C₆H₁₁ and N(C₂H₅)₂) and an improved model of [OH₈C₄N]₃P(O) are investigated. Moreover, the semi-classical density sums (PIXEL) method, which enables the calculation of interaction energies for molecule–molecule pairs, and AIM calculations were used to evaluate intermolecular forces in the studied compounds. The previously reported structure [2,6-F₂-C₆H₃C(O)NH]P(O)[NHC(CH₃)₃]₂ with a [C(O)NH]P(O)[NH(C)]₂ segment, which is different than the [C(O)NH]P(O)[N(C)(C)]₂ segment in structures?[2,3,6-F₃–C₆H₂C(O)NH]P(O)(X)₂, is compared to those of the newly determined structures. The Hirshfeld surface method shows that the crystal cohesions of structures?[2,3,6-F₃–C₆H₂C(O)NH]P(O)(X)₂ are established via H···H, O···H/H···O, C···H/H···C, and F···H/H···F contacts, while for [OH₈C₄N]₃P(O), H···H and O···H/H···O are the dominant contacts. From PIXEL and AIM calculations and the decomposition of the interaction energies for different molecular pairs, it is shown that the donor and acceptor capability of the atoms involved in an interaction introduces the nature and strength of that interaction. The more acidic N_CP–H unit in the C(O)NHP(O) segment (compared to the N_P–H unit in the P(O)[NH(C)]₂ segment) and the higher H-atom acceptor group P=O (compared to C=O) in the studied structures form the strongest N_CP–H···O=P intermolecular hydrogen bond. Graphical abstract: [Figure not available: see fulltext.].

Full text of DOI:10.1007/s00706-018-2186-y

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ORIGINAL PAPER
Synthesis and crystal structures of new phosphoric triamides: study
of intermolecular interactions by semi-empirical calculations
and Hirshfeld surface analysis
Atekeh Tarahhomi1 • Arie van der Lee2
Received: 23 January 2018 / Accepted: 14 March 2018
Ó Springer-Verlag GmbH Austria, part of Springer Nature 2018
Abstract
In the present paper, crystal structures and Hirshfeld surface analyses of two new phosphoric triamides [2,3,6-F –C H
6 2-
3
C(O)NH]P(O)(X)2 (X=N(CH )C H and N(C H ) ) and an improved model of [OH C N] P(O) are investigated.
3
3
6
11
2
5 2
8
4
Moreover, the semi-classical density sums (PIXEL) method, which enables the calculation of interaction energies for
molecule–molecule pairs, and AIM calculations were used to evaluate intermolecular forces in the studied compounds. The
previously reported structure [2,6-F -C H C(O)NH]P(O)[NHC(CH ) ] with a [C(O)NH]P(O)[NH(C)] segment, which is
2
6
3
3 3 2
2
different than the [C(O)NH]P(O)[N(C)(C)] segment in structures [2,3,6-F –C H C(O)NH]P(O)(X) , is compared to those
2
3
6
2
2
of the newly determined structures. The Hirshfeld surface method shows that the crystal cohesions of structures [2,3,6-F3–
C H C(O)NH]P(O)(X) are established via HÁÁÁH, OÁÁÁH/HÁÁÁO, CÁÁÁH/HÁÁÁC, and FÁÁÁH/HÁÁÁF contacts, while for [OH C
6
2
2
8 4-
N] P(O), HÁÁÁH and OÁÁÁH/HÁÁÁO are the dominant contacts. From PIXEL and AIM calculations and the decomposition of
3
the interaction energies for different molecular pairs, it is shown that the donor and acceptor capability of the atoms
involved in an interaction introduces the nature and strength of that interaction. The more acidic NCP–H unit in the
C(O)NHP(O) segment (compared to the N –H unit in the P(O)[NH(C)] segment) and the higher H-atom acceptor group
P
2
P=O (compared to C=O) in the studied structures form the strongest N –HÁÁÁO=P intermolecular hydrogen bond.
CP
Graphical abstract
Keywords Phosphoric triamide Á Crystal structure Á Semi-empirical calculation Á Hirshfeld surface analysis Á
N–HÁÁÁO hydrogen bond
Electronic supplementary material The online version of this article
(https://doi.org/10.1007/s00706-018-2186-y) contains supplementary
material, which is available to authorized users.
Introduction
The preparation of phosphoramides with the segment
O=)P–N such as phosphoric triamides and their crystal
&
Atekeh Tarahhomi
tarahhomi.at@semnan.ac.ir
(
growth have attracted attention because of their various
potential applications such as anticancer agents [1, 2], pro-
drugs [3, 4], urease inhibitors [5, 6], and chiral Brønsted acid
catalysts [7, 8]. Structural analysis and modeling techniques
have been used to study these phosphoramides [5, 9].
1
2
Department of Chemistry, Semnan University,
Semnan 35131-19111, Iran
Institut Europ e´ en des Membranes, IEM – UMR 5635,
ENSCM, CNRS, Universit e´ de Montpellier,
3
4095 Montpellier, France
123

A. Tarahhomi, A. van der Lee
Single-crystal X-ray diffractometry is the appropriate
method of choice for structural analysis. However, in this
method, hydrogen atoms cannot be located with accuracy
using X-rays when heavy elements are present. The exact
location of hydrogen atoms is, however, crucial for the
study of interaction energies in the fields of crystal engi-
neering and materials science [10]. A new refinement
technique called Hirshfeld Atom Refinement (HAR) [11]
was introduced for locating hydrogen atoms more accu-
rately. It uses aspherical atomic electron densities extract-
ing from a crystal-field-embedded quantum-chemical
electron density using Hirshfeld’s scheme [12].
located very accurately using Hirshfeld Atom Refinement
(HAR) in X-ray diffraction, where, for 3, HAR cannot be
used due to disorder in the structure. Furthermore, we have
employed Hirshfeld surface analysis for the three structures
1, 2, and 3 which provide a convenient means of visual-
izing and quantifying the intermolecular interactions within
the crystal structures.
Results and discussion
X-ray crystallography
Once the correct structural model has been established
by either classical or HAR refinements, the interactions
present in the 3D structure can be analyzed by different
techniques. The Hirshfeld surface analysis [13] is a useful
and powerful protocol for obtaining information on trends
in crystal packing and offers a considerable potential in
crystal engineering. This unique approach is completed
with the analysis of the associated fingerprint plots [14]
which provide insight about close contacts, more distant
contacts, and areas the positions where the interactions are
weakest.
The molecular structures of 1–3 are shown in Figs. 1, 2,
and 3. The asymmetric unit of 1 and 3 consists of one
molecule, whereas, for 2, it consists of two symmetry-in-
dependent molecules. Details of crystal data and structure
refinement have been provided in Table 1. Selected bond
distances, angles, and torsion angles are summarized in
Table 2. The structure 3 is an improved model of the
previously reported structure [OH C N] P(O) (CSD ref-
8
4
3
code BIVYAG [19]) which crystallizes in the monoclinic
centrosymmetric space group P2 /n.
1
Another interesting analysis technique for the strength
and nature of intermolecular interactions [15, 16] is based
on the calculation of lattice and interaction energies of
molecular pairs by the semi-classical PIXEL method [17].
This procedure which enables partitioning of the total
energy into electrostatic, polarization, dispersion, and
repulsion components is of such computational calcula-
tions to evaluate the importance of non-covalent interac-
tions in the crystal packing.
In all compounds, the P atom displays a distorted
tetrahedral environment and the P=O bond lengths are
standard to the related phosphoric triamide compounds
[20, 21]. In compounds
1
and
2
with
a
[C(O)NH]P(O)[N(C)(C)]2 segment, the phosphoryl and
carbonyl groups adopt an anti-orientation with respect to
one another. In each of the structures, the P–NCP bond
distance (NCP is the N atom of the segment C(O)NH-
P(O)) is significantly longer than the two other P–N bond
P
The present paper is a discussion of the structural fea-
tures of two new phosphoric triamides [2,3,6-F –C H
6 2-
distances, as resulting from the electronic effect caused by
the C(O) group, and the C–N–C angles are significantly
smaller than the two related P–N–C angles. The bond angle
sums at the tertiary nitrogen atoms of N-methylcyclo-
hexylamido group in 1 and diethylamido in 2, i.e., \P–N–
3
C(O)NH]P(O)(X)2 (X=N(CH )C H (1) and N(C H )
2 5 2
3
6
11
(
2), Scheme 1) along with evaluation of intermolecular
interactions especially the N–HÁÁÁO hydrogen bonds in
C(O)NHP(O)-based phosphoric triamides using the calcu-
lation of the lattice energy and intermolecular interaction
energies by the PIXEL method. The previously reported
structure [2,6-F -C H C(O)NH]P(O)[NHC(CH ) ] [18]
2
C ? \C–N–C ? \C–N–P, confirm the sp character of
the quoted N atoms, for example 357.09(9)° and 358.41(8)°
in the case of the N-methylcyclohexylamido group in 1.
Such N atoms do not take part in hydrogen bonding as an
acceptor, because they have a low Lewis-base character.
The hydrogen-bond patterns for structures 1 and 2 are
similar, where the anti-orientation of P=O and C=O groups
relative to one another results in a centrosymmetric (1) or
2
6
3
3 3 2
with the N –HÁÁÁO=C hydrogen bonds (N –H is the NH
P
P
unit of the segment P(O)[NH(C)] ) in the crystal structure,
2
where such hydrogen bonds (HBs) are not found in HB
patterns of 1 and 2, is analyzed as well by the PIXEL
method. Besides, AIM (Atom In Molecule) analysis is
non-centrosymmetric (2) dimer via the N –HÁÁÁO=P
CP
2
2
2
2
performed on HB-dimers of 1, 2 (both with R ð8Þ ring
hydrogen bonds forming R ð8Þ ring motif. In addition to
motif) and [2,6-F -C H C(O)NH]P(O)[NHC(CH ) ]
3 3 2
the N–HÁÁÁO hydrogen bonds, the structure of 1 is stabilized
to a lesser extent by the weak cohesion from the C–HÁÁÁO
and pÁÁÁp stacking interactions (Table 3). These interac-
tions lead to the formation of a 2D layer parallel to ac plane
composed of H-bonded dimers (Fig. 4). In the crystal
2
6
3
2
2
(
forming two consecutive dimers, one with an R ð8Þ ring
2
2
1
2
motif and another with an R ð12Þ/R ð6Þ motif). An
improved model of [OH C N] P(O) (3) [19] (Scheme 1) is
3
8
4
also reported. Hydrogen atoms in structures 1 and 2 are
1
23

Synthesis and crystal structures of new phosphoric triamides: study of intermolecular…
structure of 2, the non-centrosymmetric dimers are con-
nected through the C–HÁÁÁO, pÁÁÁp stacking and HÁÁÁH
interactions (Table 3) leading to a 2D layer parallel to
A simple review of the lattice energies reported in
Table 4 imparts that the highest values are found for
phosphoric triamides and with the segment
[C(O)NH]P(O)[N(C)(C)] , then, [C(O)NH]P(O)[tert-Bu]
1
2
(
111) plane (Fig. 5).
2
2
Structure 3 does not have any N–HÁÁÁO strong hydrogen
with the segment [C(O)NH]P(O)[NH(C)] and eventually,
2
bonds resulting from the absence of any N–H units. The
3 with the segment P(O)[N(C)(C)] . This is an expected
3
crystal stabilization is produced via C–HÁÁÁO interactions
result as the crystal cohesions of 1 and 2 are stabilized by
the strong N –HÁÁÁO=P hydrogen bonds, while, for
CP
(
Table 3) which extend the structure to a three-dimensional
network.
[C(O)NH]P(O)[tert-Bu] , the slightly weaker N–HÁÁÁO
2
(
N –HÁÁÁO=C and N –HÁÁÁO=P) hydrogen bonds relative
P
CP
Evaluation of N–H…O hydrogen bonds
by intermolecular interaction energies
and topological properties
to N –HÁÁÁO=P in 1 and 2 are involved in crystal packing.
CP
Finally, in the crystal structure of 3, there is no strong
hydrogen bond. In this way, the results of lattice energy
calculations confirm the obtained findings of the statistical
analysis on the strength of N–HÁÁÁO hydrogen bonds in
phosphoric triamides [22, 23].
The lattice energies of 1–3 and the previously reported
structure [2,6-F -C H C(O)NH]P(O)[NHC(CH ) ] ([C(O)
2
6
3
3 3 2
NH]P(O)[tert-Bu] ) calculated using the PIXEL method
2
To further evaluate the N–HÁÁÁO hydrogen bonds, dif-
ferent intermolecular interactions in 1–3 and [C(O)NH]-
P(O)[tert-Bu]2 along with geometrical parameters,
symmetry, and interaction energies partitioned into differ-
ent energy components are presented in Table 5. The
molecular pairs involved in the crystal packing of 1–3 and
are presented in Table 4. Energy partitioning shows that,
for all compounds, the major contributions towards the
lattice stabilization originate from the coulombic and dis-
persion components, while the remaining contribution is
afforded by the polarization energy.
123

A. Tarahhomi, A. van der Lee
Fig. 1 ORTEP-style plot and
atom-labeling scheme for
structure 1. Displacement
ellipsoids are drawn at the 50%
probability level and H atoms
are drawn as circles of arbitrary
radii
Fig. 2 ORTEP-style plot and
atom-labeling scheme for
structure 2, showing two
independent molecules P1 and
P29. Displacement ellipsoids
are drawn at the 50%
probability level and H atoms
are drawn as circles of arbitrary
radii
1
23

Synthesis and crystal structures of new phosphoric triamides: study of intermolecular…
Fig. 3 ORTEP-style plot and
atom-labeling scheme for
structure 3. Displacement
ellipsoids are drawn at the 50%
probability level and H atoms
are drawn as circles of arbitrary
radii. Bonds connecting
disordered atoms with minor
components are shown as dash
lines
[
C(O)NH]P(O)[tert-Bu] and corresponding intermolecular
2
hydrogen bond, i.e., coulombic interactions dominate
before the polarization and dispersion contributions. Other
molecular pairs have weak interactions such as C–HÁÁÁO
and pÁÁÁp interactions with energies less than
- 48.0 kJ/mol (Table 5). In this way, the results show that
interactions considered in interaction energies calculations
are shown in Figs. 6 and 7.
In 1, 2, and [C(O)NH]P(O)[tert-Bu] , the most
2
stable molecular pairs observed are the hydrogen-bonded
dimers of N –HÁÁÁO=P having a stabilization energy of
CP
in 1, 2, and [C(O)NH]P(O)[tert-Bu] with at least one N–H
2
-
116.3, - 122.5, and - 96.8 kJ/mol, respectively. The
unit, the N–HÁÁÁO hydrogen bonds are the most important
stability of these molecular pairs is provided by the
intermolecular interactions.
coulombic contribution (52% for 1 and 2, and 47% for
C(O)NH]P(O)[tert-Bu] ), followed by polarization (26%
Moreover, in 1 and 2, the N –HÁÁÁO=P hydrogen bonds
CP
[
contribute more to the lattice energy than the N –HÁÁÁO=C
2
P
for 1 and 2, and 33% for [C(O)NH]P(O)[tert-Bu] ) and
2
hydrogen bonds in [C(O)NH]P(O)[tert-Bu] These results
2.
dispersion (22% for 1 and 2, and 21% for [C(O)NH]-
P(O)[tert-Bu] ) components, respectively (Table 5). In
are in agreement with those obtained from other reported
analyses on the N–HÁÁÁO hydrogen bonds in C(O)NHP(O)-
based phosphoric triamides [22, 23] which show that the
N –HÁÁÁO=P hydrogen bond is stronger than the N –
2
[
C(O)NH]P(O)[tert-Bu] , the coulombic interactions are
2
smaller and the polarization contributions are larger than in
and 2, respectively. This can be attributed to the lower
strength of the N –H…O=P hydrogen bond in
CP
P
1
HÁÁÁO=C hydrogen bond.
Finally, for 3, the most stable molecular pair (I) has an
interaction energy being - 40.6 kJ/mol (Table 5), where
the structure only include the C–HÁÁÁO hydrogen bonds
without any N–HÁÁÁO interaction as a result of the lack of
the N–H unit in this structure. The stability of this
molecular pair is driven mainly by dispersion forces (55%),
and then by coulombic (28%) and polarization (17%)
contributions, respectively.
CP
[
(
[
C(O)NH]P(O)[NH(C)] -based
phosphoric
triamides
2
[C(O)NH]P(O)[tert-Bu]2)
compared to
that in
C(O)NH]P(O)[N(C)(C)] -based phosphoric triamides (1
2
and 2) [22, 23].
In [C(O)NH]P(O)[tert-Bu]2,
the
next
most
stable molecular pair contains the N –HÁÁÁO=C hydrogen
P
bond whose interaction energy is calculated to be
-
81.4 kJ/mol. In this molecular pair, the strength order of
The N–HÁÁÁO hydrogen bonds were also analyzed by a
Quantum Theory of Atom In Molecule (QTAIM) analysis
the contributions is the same as in the N –HÁÁÁO=P
CP
123

A. Tarahhomi, A. van der Lee
Table 1 Crystal data and
structure refinement for
compounds 1–3
1
2
3
Empirical formula
-
Mr/g mol
C
21
H
31 3
F N
3 2
O P
C
15
H
23 3
F N
3 2
O P
12 24 3 4
C H N O P
1
445.46
175
365.33
175
305.31
175
T/K
˚
k/A
0.71073
0.71073
0.71073
Monoclinic
P2 /n
Crystal system
Space group
Triclinic
Triclinic
P 1ꢀ
P 1ꢀ
1
˚
a/A
10.2200(3)
10.6530(4)
11.3031(5)
69.721(3)
79.415(3)
81.464(3)
1129.89(5)
2
10.0500(5)
10.4670(5)
9.1334(4)
11.1786(5)
14.6624(6)
90
˚
b/A
˚
c/A
19.5123(10)
78.668(4)
80.643(4)
63.230(5)
1790.39(9)
4
a/8
b/8
c/8
96.979(4)
90
3
˚
V/A
1485.92(6)
4
Z
-3
Density/g cm
1.309
1.355
1.365
-
1
l/mm
F(000)
Crystal size/mm
Crystal color/habit
0.168
0.196
0.202
472
768
656
3
0.10 9 0.40 9 0.50
Colorless/thick plate
0.045
0.35 9 0.47 9 0.55
Colorless/prism
0.043
0.22 9 0.40 9 0.45
Colorless/prism
0.048
R
int
Qmax/8
32.665
29.265
29.075
˚
Resolution/A
0.66
0.73
0.73
N
N
N
N
N
tot (measured)
40,799
17,694
15,826
ref (unique)
7721
8266
3624
ref (I [ 2r(I))
ref (least-squares)
6583
6225
3023
7716
8264
3622
par
274
433
254
\s(I)/I[
0.0516
0.0638
0.0596
R
1, wR
2
(I [ 2r(I))
(all)
0.0424, 0.0909
0.0528, 0.0989
0.9062
0.0540, 0.1319
0.0771, 0.1548
0.9028
0.0501, 0.0655
0.0638, 0.0700
0.9960
R
1
, wR
2
GOF
-3
˚
Dr/e A
- 0.40/0.45
- 0.47/0.63
- 0.35/0.39
using AIM2000 on dimers of 1, 2, and [C(O)NH]P(O)[tert-
Bu] for obtaining the bond critical points (BCPs) between
values of HÁÁÁO contacts for N –HÁÁÁO=P hydrogen bonds
CP
shows that these values for [C(O)NH]P(O)[tert-Bu] are
2
2
the interacting atoms and, then, the topological parameters
2
slightly lower than those in 1 and 2. On the basis of this
observation, it is deduced that the NCP–HÁÁÁO=P hydrogen
q(r) and L(r) (= - r q ). The dimers have a N –HÁÁÁO=P
ðrÞ
CP
2
bond in phosphoric triamides with
a
segment
hydrogen bond inside the R ð8Þ ring motif for 1 (molecular
2
[
C(O)NH]P(O)[N(C)(C)]2 (such as 1 and 2) is slightly
stronger than that in phosphoric triamides with a
[C(O)NH]P(O)[NH(C)] segment (such as [C(O)NH]P(O)[-
tert-Bu] ). Finally, the results reveal that the N –H unit and
pair I in Fig. 6, left), 2 (molecular pair I in Fig. 6, right) and
[
C(O)NH]P(O)[tert-Bu] (molecular pair I in Fig. 7, right),
2
2
2
2
and the N –HÁÁÁO=C/R ð12Þ hydrogen bond (molecular pair
P
2
CP
II in Fig. 7, right) for [C(O)NH]P(O)[tert-Bu] . As can be
2
the P=O group take part in stronger N–HÁÁÁO hydrogen bonds
seen in Table 6, the q(r) and L(r) values of HÁÁÁO contacts for
compared to the N –H unit and the C=O group, respectively.
P
N –HÁÁÁO=P hydrogen bonds in 1, 2, and [C(O)NH]P(O)[-
CP
This demonstrates the more acidic character of the proton in
N –H compared to that in N –H due to the resonance
tert-Bu] are higher than those for N –HÁÁÁO=C hydrogen
2
P
CP
P
bond in [C(O)NH]P(O)[tert-Bu] , confirming the higher
2
interaction of NCP lone pair with the C=O bond and the higher
H-atom acceptor capability of OP=O compared to OC=O
strength of the HÁÁÁO interaction in N –HÁÁÁO=P than in N –
CP
P
.
HÁÁÁO=C [22, 23]. Moreover, a comparison of the q and L
(
r)
(r)
1
23

Synthesis and crystal structures of new phosphoric triamides: study of intermolecular…
Table 2 Selected bond
Compound 1
˚
distances (A) and angles (°) for
compound 1–3
P1–O2
P1–N3
1.4860(8)
1.6322(9)
1.6886(9)
1.6331(11)
1.2148(14)
N3–P1–O2
N11–P1–O2
N23–P1–O2
N3–P1–N11
N3–P1–N23
110.60(5)
105.22(5)
117.11(6)
112.59(5)
105.64(5)
N11–P1–N23
105.76(5)
2.4(2)
O13–C12–N11–P1
O2–P1–N11–C12
N3–P1–N11–C12
N23–P1–N11–C12
P1–N11
164.0(1)
43.5(1)
P1–N23
C12–O13
Compound 2
P1–O2
- 71.4(1)
1.4822(17)
1.4821(18)
1.628(2)
1.632(2)
1.688(2)
1.696(2)
1.634(2)
1.628(2)
1.212(3)
1.213(3)
N3–P1–O2
116.87(12)
109.74(11)
106.02(10)
106.80(12)
104.24(11)
113.25(11)
105.41(10)
109.85(11)
117.01(12)
112.23(11)
N31–P29–N36
104.85(11)
107.49(12)
- 2.4(4)
- 159.6(2)
76.5(3)
P29–O30
P1–N3
N9–P1–O2
N33–P29–N36
N15–P1–O2
N3–P1–N9
O17–C16–N15–P1
O2–P1–N15–C16
N3–P1–N15–C16
N9–P1–N15–C16
O46–C45–N31–P29
O30–P29–N31–C45
N33–P29–N31–C45
N36–P29–N31–C45
P1–N9
P1–N15
N3–P1–N15
N9–P1–N15
N31–P29–O30
N33–P29–O30
N36–P29–O30
N31–P29–N33
P29–N31
P29–N33
P29–N36
C16–O17
C45–O46
Compound 3
P11–O21
P10–O20
P11–N30
P10–N31
P11–N13
P11–N19
N30–P11–O21
- 39.2(3)
- 7.2(4)
- 158.6(2)
- 39.1(3)
77.3(2)
1.480(10)
1.488(11)
1.694(12)
1.602(13)
1.617(10)
1.709(9)
N20–P10–O31
N13–P11–O21
N19–P11–O21
N13–P11–N19
N13–P11–N30
N19–P11–N30
N13–P10–N19
121.1(7)
109.5(6)
108.7(7)
113.5(5)
103.4(6)
103.5(6)
113.2(6)
N13–P10–N31
100.3(7)
103.0(7)
- 30.2(7)
35.6(7)
N19–P10–N31
O21–P11–N13–C18
O21–P11–N19–C24
O21–P11–N30–C4
O20–P10–N31–C5
92.0(1)
85.0(1)
118.2(6)
Study of intermolecular interactions by Hirshfeld
surface analysis
white areas to which show that such interactions are rather
weak.
In the HS of 3 (Fig. 12), the C–HÁÁÁO hydrogen bonds
from the interactions between the O atoms (of P=O group
The Hirshfeld surfaces (HSs) of 1, molecules P1 and P29 of
2
˚
, and 3 mapped over the dnorm range of - 0.18 to 1.61 A
or NC H O rings) and CH groups (of NC H O rings)
4 8 4 8
are shown in Figs. 8, 9, 10, 11, and 12 and S1–S3. HSs
mapped over the shape index for 1 and molecules P1 and
P29 of 2 are given in Figs. 9, 11, and S2. For 3 that shows
disorder in the P=O group and one of morpholine rings, the
HSs were separately generated for both possible major
(Table 3) appear as red areas. No other characteristic
contacts as red spots are seen on the HS.
Figures 8, 9, 10, 11, 12, S1–S3 also show the FPs of 1–
3. These plots are the graphical views with the d and d
e i
distance scales which analyze the intermolecular contacts
and their contributions to the corresponding total HS at the
same time.
(
Fig. 12) and minor (Fig. S3) components. The interaction
proportions for the two models are nearly the same having
a variability of less than 0.5%; hence, for the following
discussion, the major component in 3 is discussed only and
is treated as fully occupied.
An important feature of the FPs is that they are rather
symmetric for 1 and 3, while they have slightly asym-
metrical shapes especially in the upper areas of the plots for
two independent molecules of 2. This highlights the iso-
tropic environment of molecules in the solid state of 1 and
3 [24], whereas two molecules P1 and P29 present in
crystal 2 are involved in slightly different intermolecular
interaction patterns.
For 1 and both molecules of 2, the dominant interactions
between the N–H unit and phosphoryl O atom (Table 3)
can be seen in the corresponding HSs as the deep red spots
shown in Figs. 8, 10, and S1. In these HSs, the light red
spots are due to C–HÁÁÁO=P interactions (Table 3). In 1,
other visible spots on the HS are the small pale red spots
which correspond to C–HÁÁÁO=C contacts (Table 3),
reflecting the smaller H-atom acceptor capability of C=O
relative to P=O. In Figs. 9, 11, and S2, the C–HÁÁÁF
hydrogen bonds (black dash lines) can be recognized as
The FPs reveal that the main intermolecular interactions
in 1–3 are HÁÁÁH contacts which are a common feature of
phosphoric triamide molecular crystals [20] and cover most
of the area in the plots with the most significant contribu-
tion to the total HSs (57.4% for 1, 48.1% for molecule P1
123

A. Tarahhomi, A. van der Lee
Table 3 Hydrogen bonds and
short contacts’ geometries (A, °)
for compounds 1–3
D–H…A
d(D–H)
d(H…A)
d(D…A)
\(DHA)
˚
Compound 1
i
N11–H111ÁÁÁO2
0.858
0.986
0.972
0.944
–
1.894
2.535
2.607
2.375
–
2.736(2)
3.465(2)
3.511(2)
3.138(2)
3.6854(1)
166.5
157.2
154.9
137.7
–
ii
C9–H92ÁÁÁO13
ii
C10–H101ÁÁÁO13
iii
C20–H201ÁÁÁO2
*
Cg…Cg
Compound 2
N15–H151ÁÁÁO30
N31–H311ÁÁÁO2
0.832
0.848
0.920
0.922
–
1.928
1.940
2.412
2.484
2.3477
–
2.749(5)
2.779(5)
3.251(3)
3.213(4)
–
168.6
169.7
151.7
136.2
–
i
C50–H501ÁÁÁO2
ii
C21–H211ÁÁÁO30
C11–H112ÁÁÁH371–C37
Cg…Cg
iii
–
4.0260(2)
4.0666(2)
–
à
Cg…Cg
Compound 3
–
–
–
i
C20–H201ÁÁÁO21
0.955
0.958
0.958
0.959
0.968
0.962
2.318
2.467
2.702
2.642
2.673
2.600
3.134(8)
3.352(4)
3.605(2)
3.580(5)
3.630(5)
3.291(5)
143.0
153.5
157.3
166.0
170.3
128.9
ii
C11–H112ÁÁÁO22
ii
C17–H171ÁÁÁO22
iii
C14–H142ÁÁÁO80
iii
C20–H202ÁÁÁO80
iv
C4–H42ÁÁÁO16
Symmetry transformations used to generate equivalent atoms for 1: (i): - x ? 1, -y ? 2, -z; (ii):
-
-
-
x ? 1, -y ? 2, -z ? 1; (iii): x - 1, y, z; for 2: (i): - x ? 1, - y ? 2, - z ? 1; (ii): - x ? 1,
3
1
3
1
y ? 1, - z ? 2; (iii): x - 1, y ? 1, z; for 3: (i): - x ? , y ? , - z ? ; (ii) x - 1, y, z; (iii) x ? ,
1
2
2
2
2
1
1
1
1
y ? , z ? ; (iv): x ? , - y ? , z -
2
2
2
2
2
*
Cg = centroid of the phenyl ring of molecule 1
Cg = centroid of the phenyl ring of molecule P29 of 2
Cg = centroid of the phenyl ring of molecule P1 of 2
à
Fig. 4 Partial crystal packing
diagram for 1 is shown. 2D
layer parallel to ac plane is
formed via C–H…O (orange
dashed lines) and p…p stacking
interactions (Table 3)
connecting the centrosymmetric
N–H…O=P dimers (black
dashed lines). H, P, O, and N
atoms involved in N–H…O
contacts are shown as ‘‘small
balls’’ and the other H atoms
bonded to C atoms have been
omitted for clarity
1
23

Synthesis and crystal structures of new phosphoric triamides: study of intermolecular…
Fig. 5 Part of the crystal
packing of structure 2, adjacent
molecules are linked via the
H…O and H…H interactions
(
black dashed lines), and p…p
stacking (Table 3) composed of
H-bonded dimers, forming a 2D
layer parallel to (111) plane. H,
P, O, and N atoms involved in
N–H…O contacts are shown as
‘‘small balls’’ and the other H
atoms bonded to C atoms have
been omitted for clarity
Table 4 Lattice energies of
compounds 1–3 and
Compound
coul
E /
kJ mol
pol
E /
kJ mol
E
kJ mol
disp
/
E
rep
/
kJ mol
tot
E /
-1
-1
-1
-1
-1
kJ mol
[
C(O)NH]P(O)[tert-Bu]
2
partitioned into different energy
components
1
2
3
- 112.8
- 103.3
- 79.4
- 48.7
- 44.2
- 35.8
- 41.9
- 183.1
- 150.6
- 154.1
- 143.4
177.5
141.0
143.9
132.5
- 167.1
- 157.2
- 125.4
- 155.4
[
C(O)NH]P(O)[tert-Bu]
2
- 102.6
of 2, 44.4% for molecule P29 of 2, and 72.8% for 3). These
contacts provide the closest interactions with d ? d
spikes to the plot diagonal. The middle ones with the
˚
closest contact near 2.1 A which are longer than the other
i
e-
˚
2.3 A for 1, 2.2 A for both molecules P1 and P29 of 2,
˚
[
and 2.1 A for 3, showing a short broad (1 and 3) or thin
two pair spikes (the close and far ones) are probable
resulting from the C–HÁÁÁO=P hydrogen bonds, where the
O atom of P=O is a better H-bond acceptor than the O atom
of the NC H O rings.
˚
(
both P1 and P29 of 2) spike on the plot diagonal.
In the decomposed HÁÁÁH FPs, the other important point
4
8
is the color change from blue to green in the region of
˚
The points in the (d , d ) regions of the top left
e i
˚
˚
˚
˚
1
.2 A \ d , d \ 1.8 A for 1 and P29 of 2, 1.1 A \ d ,
(1.7–2.6 A, 1.2–2.0 A, d [ d ) and the bottom right
e
i
e
e
i
˚
˚
˚
˚
˚
d \ 1.6 A for P1 of 2, and 1.4 A \ d , d \ 1.9 A for 3,
(1.2–2.2 A, 1.7–2.7 A, d \ d ) in the FP of 1 are due to
i
e
i
e
i
which show that the occurrence frequency of HÁÁÁH con-
CÁÁÁH/HÁÁÁC interactions (Fig. 8), having a 7.3% contribu-
tion to the total interactions. For 2, similar regions on the
FPs appearing as wings are found for CÁÁÁH/HÁÁÁC contacts
(Figs. 10 and S1), 10.9% contribution [top left (1.7–2.5,
tacts is increased in the mentioned regions.
For 1 and 2, prominent pairs of sharp spikes with almost
˚
˚
equal lengths in the region 1.7 A \ d ? d \ 2.6 A of the
e
i
˚
1.1–2.0 A) and bottom right (1.1–2.4, 1.7–2.8 A] for
˚
FPs (Figs. 8, 10, and S1) are characteristics of OÁÁÁH/HÁÁÁO
contacts made from the N–HÁÁÁO=P, C–HÁÁÁO=P, and C–
HÁÁÁO=C hydrogen bonds. These OÁÁÁH/HÁÁÁO contacts
comprise a 10.6% (1) and a 13.4% (P1 and P29 of 2)
contribution to the corresponding HSs. As can be deduced
from the figures, the upper spike corresponds to the donor
spike (H atoms from N–H or C–H interacting with O atoms
of P=O or C=O groups), with the lower spike being an
acceptor spike (O atoms from P=O or C=O groups inter-
acting with the H atoms of N–H or C–H).
˚
molecule P1 and 9.5% [(1.7–2.7, 1.1–2.2 A) and (1.1–2.0,
˚
1.7–2.5 A)] for P29.
For 1 and 2, the FÁÁÁH/HÁÁÁF contacts (21.7% for 1,
25.1% for P1 of 2, and 30.1% for P29 of 2) show up in the
upward middle of scattered points in the corresponding
plots. For 1, the mentioned area contains two symmetric
broad spikes at left and right bottom sections of the plot
˚
with minimum d ? d values of 2.6 A, whereas these
e
i
spikes become very short or thin in FÁÁÁH/HÁÁÁF FPs of
molecules P1 and P29 of 2.
For 3, the C–HÁÁÁO intermolecular interactions (OÁÁÁH/
HÁÁÁO contacts, 27.0%) appear as three pair moderate dis-
tinct spikes in the 2D FP (Fig. 12): the close (in the region
The CÁÁÁC FP of 1 (1.4% contribution, in the region
˚
˚
1.6 A \ d , d \ 2.1 A) and molecules P1 (1.2%,
e
i
˚
˚
˚
˚
˚
˚
2
.2 A \ d ? d \ 2.8 A),
middle
(2.1 A \ d ? d
1.7 A \ d , d \ 2.2 A) and P29 (1.3%, 1.7 A \ d , d
e
i
e
i-
e
i
e
i-
˚
˚
˚
˚
\
2.7 A), and far (2.3 A \ d ? d \ 2.8 A) double
\ 2.1 A) of 2 in Figs. 9, 11, and S2 show the
e
i
123

A. Tarahhomi, A. van der Lee
Table 5 List of intermolecular interaction energies (kJ/mol) for short contacts of 1–3 and [C(O)NH]P(O)[tert-Bu]
2
Molecular Interactions
pairs
Symmetry code
X…A/
D–
Centroid…Centroid
E
coul
E
pol
E
disp
E
rep
E
tot
˚
˚
A
X…A/ Distance/A
°
Compound 1
I
N11–H111ÁÁÁO2 - x ? 1, - y ? 2, 1.894
166.5
157.2
154.9
5.234
6.574
6.574
- 133.8 - 56.1 - 66.8 140.3 - 116.3
-
z
II
II
C9–H92ÁÁÁO13
- x ? 1, - y ? 2, 2.535
z ? 1
- 19.6
- 19.6
- 9.6 - 56.3
- 9.6 - 56.3
38.2
38.2
- 47.3
- 47.3
-
C10–
- x ? 1, - y ? 2, 2.607
- z ? 1
H101ÁÁÁO13
III
IV
C20–H201ÁÁÁO2 x - 1, y, z
2.375
137.7
–
10.220
9.198
- 24.5
- 0.6
- 9.8 - 28.9
- 5.4 - 44.3
28.0
31.4
- 35.3
- 18.9
C19…C21
p…p)
- x ? 2, - y ? 2, 3.685
- z
(
Compound 2
I
N15–
H151ÁÁÁO30
N31–H311ÁÁÁO2 x, y, z
x, y, z
1.928
1.940
168.6
4.979
- 133.9 - 57.4 - 65.9 134.8 - 122.5
- 133.9 - 57.4 - 65.9 134.8 - 122.5
I
169.7
136.2
4.979
II
C21–
H211ÁÁÁO30
C11–
H112ÁÁÁH371–
C37
C50–H501ÁÁÁO2 - x ? 1, - y ? 2, 2.412
z ? 1
- x ? 1, - y ? 1, 2.484
10.010
- 22.4
- 9.2 - 26.7
24.6
- 33.8
- z ? 2
III
x ? 1, y - 1, z
2.3477
–
6.439
- 10.1
- 6.3 - 43.1
26.9
- 32.6
IV
V
151.7
–
10.270
8.918
- 20.8
0.1
- 7.2 - 16.7
- 3.5 - 30.9
- 3.7 - 27.9
16.5
19.4
16.8
3.7
- 28.2
- 14.9
- 14.0
- 7.9
-
C48…C51
p…p)
C19…C22
p…p)
C38–
H381ÁÁÁF55
- x ? 1, - y ? 2, 4.026
- z ? 1
(
VI
VII
- x ? 1, - y ? 1, 4.067
- z ? 2
–
9.036
0.7
(
x - 1, y, z
2.663
138.7
10.066
- 1.4
- 0.7
- 9.6
Compound 3
3
1
2
I
C20–
H201ÁÁÁO21
C14–
H142ÁÁÁO80
C20–
H202ÁÁÁO80
- x ? , y - ,
2.318
2.642
2.673
143.0
166.0
170.3
5.790
8.370
8.370
- 21.2 - 12.3 - 41.1
34.0
15.1
15.1
- 40.6
- 25.4
- 25.4
2
z ? 3
2
-
1
1
2
II
II
x - , - y ? ,
- 13.5
- 13.5
- 4.4 - 22.7
- 4.4 - 22.7
2
z - 1
2
1
2
1
2
x ? , - y ? ,
1
z ? ,
2
III
III
IV
C11–
H112ÁÁÁO22
C17–
H171ÁÁÁO22
C4–H42ÁÁÁO16
x - 1, y, z
2.467
2.702
2.600
153.5
157.3
128.9
9.133
9.133
9.291
- 10.5
- 10.5
- 7.6
- 4.8 - 22.2
- 4.8 - 22.2
- 3.6 - 22.2
18.9
18.9
17.3
- 18.6
- 18.6
- 16.1
x - 1, y, z
1
1
2
x - , - y ? ,
2
z ? 1
2
[
C(O)NH]P(O)[tert-Bu]
2
I
N1–H1 NÁÁÁO2
- x, - y ? 1,
z ? 1
- x, - y ? 1,
z ? 1
- x ? 1, - y ? 1, 2.22(1)
z ? 1
- x ? 1, - y ? 1, 2.22(2)
z ? 1
1.96(1)
172(2) 4.807
– 4.807
- 99.7 - 44.2 - 69.5 116.5
- 99.7 - 44.2 - 69.5 116.5
- 96.8
- 96.8
- 81.4
- 81.4
-
I
C5ÁÁÁO2
3.179(3)
-
II
II
N2–H2 NÁÁÁO1
N3–H3 NÁÁÁO1
160(2) 5.322
152(2) 5.322
- 71.8 - 26.0 - 57.6
- 71.8 - 26.0 - 57.6
74.1
74.1
-
-
1
23

Synthesis and crystal structures of new phosphoric triamides: study of intermolecular…
Fig. 6 View of crystal packing of 1 (left) and 2 (right) showing molecular pairs and corresponding intermolecular interactions considered in
interaction energies calculations
Fig. 7 View of crystal packing of 3 (left) and [C(O)NH]P(O)[tert-Bu]
interactions considered in interaction energies calculations
2
(right) showing molecular pairs and corresponding intermolecular
characteristic motifs defined as a stacking kite on the
middle plot due to the presence of CÁÁÁC interactions
between unsaturated C atoms such as pÁÁÁp interactions.
These interactions are also reflected by red–blue triangles
on the shape index surfaces of 1 and molecules P1 and P29
of 2 in Figs. 9, 11, and S2. Where HS mapped with the
shape index, as a feature of HS analysis allowing for the
identification of complementarity between molecules in the
crystal packing structure, can be used to identify charac-
teristic packing modes, in particular planar stacking
arrangements and the presence of aromatic stacking inter-
actions such as C–HÁÁÁp and pÁÁÁp interactions [25].
123

A. Tarahhomi, A. van der Lee
Table 6 N–H…O hydrogen
bonds (A) and topological
properties (in a.u.) for the atoms
involved in the hydrogen bonds
for compounds 1, 2, and
˚
Compound/graph set type of hydrogen bond
d(D…A)/A experimental
q(r)/L(r) at the BCP/a.u.
H…O
˚
2
2
1
/ R ð8Þ
N
CP–H…O(P)
2.736(2)
0.027/- 0.027
[
C(O)NH]P(O)[tert-Bu]
calculated at the MP2/6-
1G(d,p)
2
,
2
2/ R ð8Þ
2
3
N
CP–H…O(P)
2.749(5)
2.779(5)
0.024/- 0.023
0.025/- 0.025
N
CP–H…O(P)
C(O)NH]P(O)[tert-Bu]
2
2
2
2
[
2
/R ð8Þ=R ð12Þ
N
N
N
CP–H…O(P)
2.808(2)
3.042(2)
3.008(2)
0.023/- 0.022
0.012/- 0.012
0.013/- 0.013
P
–H…O(C)
–H…O(C)
P
The average values is reported
Conclusions
beside structures 1 and 2. The main features from these
investigations are: (a) the HS analysis results show that the
molecular interactions in 1 and 2 are dominated by HÁÁÁH
and FÁÁÁH/HÁÁÁF interactions (non-red areas on HSs) which
together account for 73–80% of the HS. Whereas the
contribution of the OÁÁÁH/HÁÁÁO, appeared as red spots and
CÁÁÁH/HÁÁÁC contacts altogether, is less than 25%. For 3,
especially HÁÁÁH and OÁÁÁH/HÁÁÁO contacts (red spots on the
HS) contribute to the crystal cohesion; (b) from PIXEL
X-ray crystallography study, Hirshfeld surface (HS) anal-
ysis, and semi-empirical calculation using the PIXEL
method for two new C(O)NHP(O)-based phosphoric tri-
amides (1 and 2) and an improved model of [OH C N]
3-
8
4
P(O) (3) were presented here. Moreover, a previously
reported structure [2,6-F -C H C(O)NH]P(O)[NHC
CH ) ] was modeled for PIXEL and AIM calculations
2
6 3
(
3
3 2
Fig. 8 Up: dnorm Hirshfeld surface surrounded by neighboring
molecules associated with close contacts for 1 in two different
orientations. Down: decomposed fingerprint plots and percentage
contributions to the total HS for intermolecular contacts H…H,
O…H/H…O, and C…H/H…C for 1. The full fingerprint plot appears
as a grey shadow below each decomposed plot
1
23

Synthesis and crystal structures of new phosphoric triamides: study of intermolecular…
Fig. 9 Up: dnorm Hirshfeld surface in two different orientations (left
and middle) and Hirshfeld surface mapped with shape index (right),
surrounded by neighboring molecules associated with close contacts
H…F/F…H (black dash lines, white areas) or p…p stacking, for 1.
Down: decomposed fingerprint plots and percentage contributions to
the total HS for intermolecular contacts F…H/H…F and C…C for 1.
The full fingerprint plot appears as a grey shadow below each
decomposed plot
calculations, it is revealed that coulombic contribution
plays a dominating role in the lattice energy for strong
hydrogen bonds N –HÁÁÁO=P and N –HÁÁÁO=C, while for
Crystal structure determination
CP
P
A suitable single crystal for each of the compounds 1–3
was selected for the X-ray diffraction experiment and
mounted on a glass fiber.
weak interactions such as C–HÁÁÁO interactions, the dis-
persion contribution becomes a dominating factor; (c) the
results obtained from PIXEL and AIM calculations show
For structures 1–3, measurements were made on a
Gemini diffractometer with graphite monochromated Mo
that the N –HÁÁÁO=P hydrogen bond has a higher strength
CP
˚
than the N –HÁÁÁO = C; (d) all obtained results give evi-
Ka radiation (k = 0.7107 A) and equipped with a Sap-
P
dences for the importance of strong N–HÁÁÁO interactions in
molecular assemblies of phosphoric triamides, while, at the
same time, the weaker interactions play a decisive role in
the crystal packing.
phire3 CCD detector. The data were corrected for
absorption using redundant reflections with CrysAlisPro
[26]. Structures were solved using the charge-flipping
method implemented in the Superflip program [27] and
refined using the CRYSTALS program [28]. Non-H atoms
were refined anisotropically. After that, the H atoms were
all located in the difference Fourier maps for each of
structures, but those attached to C atoms were repositioned
geometrically. The H atoms were initially refined with soft
restraints on the bond lengths and angles to regularise their
Experimental
All chemicals were of analytical grade, obtained from
commercial sources and used without purification. Infrared
˚
geometry (C–H in the range 0.93–0.98 A and N–H in the
˚
range 0.86–0.89 A), after which the positions were refined
(
IR) spectra were recorded on a Bruker ALPHA FT-IR
1
spectrometer using a KBr disk. H, C, P{ H}, and
13
31
1
1
9
1
F{ H} NMR spectra were recorded on an FT-NMR
with riding constraints [29] and fixed isotropic displace-
1
Bruker Avance DRX 400 spectrometer, using TMS for H
19
and C, 85% H PO for P, and CF Cl for F (as internal
ment parameters U (H) = 1.5U (C ) for CH groups or
iso
eq
i
3
1
3
31
3
4
3
1.2U (C ) for CH and CH groups, where U (C ) and
eq ii 2 eq i
standards).
U (C ) are the equivalent displacement parameters of the
eq ii
C atoms to which corresponding H atoms are bonded.
123

A. Tarahhomi, A. van der Lee
Fig. 10 Up: dnorm Hirshfeld surface surrounded by neighboring
molecules associated with close contacts for molecule P1 of 2 in
two different orientations. Down: decomposed fingerprint plots and
percentage contributions to the total HS for intermolecular contacts
H…H, O…H/H…O and C…H/H…C for molecule P1 of 2. The full
fingerprint plot appears as a grey shadow below each decomposed
plot
CCDC numbers 1541709, 1541710 and 1541711 for
three reported structures 1–3 contain the supplementary
crystallographic data for this paper. These data can be
obtained free of charge from Cambridge Crystallographic
Data Centre via http://www.ccdc.cam.ac.uk/data_request/
cif.
structure 114.53°. The largest distance difference between
˚
the two structures is also for H111, i.e., 0.16 A. For a very
accurate description of the hydrogen-bond interactions in a
structure, it is thus preferable to use a HAR. However, just
because of the ADP’s of the hydrogens involved in
hydrogen-bond interactions in 2 are non-positive definite,
we prefer to use the classical description for the discussion
below. For the details of the HAR refinements, see the
supplementary material of this paper (Table S1 and
Figs. S4 and S5). The arithmetic mean of the distance
A Hirshfeld Atomic Refinement (HAR) was also per-
formed for the two non-disordered structures. As can be
seen from Table S1, the refinement are considerably
improved, from R = 0.0528 to R = 0.0327 for structure 1,
1
1
˚
between the two models for structure 1 is 0.0631 A and
and from R = 0.0771 to R = 0.0568 for structure 2. The
1
1
˚
that for structure 2 0.0699 A. The measures of similarity
are 0.009 for both 1 and 2. Without hydrogen atoms, the
˚
arithmetic means of the distance difference are 0.0044 A
˚
and 0.0057 A for 1 and 2, respectively, and the similarity
indices 0.001 for both 1 and 2.
positional and anisotropic Atomic Displacement Parame-
ters (ADP) of all hydrogen atoms were refined, giving
realistic ‘neutron’ carbon and nitrogen to hydrogen dis-
tances. For 2, the ADPs of the hydrogen atoms bounded to
nitrogen appeared to be non-positive definite, showing still
some shortcomings in either the data quality or the crystal-
field-embedded quantum-chemical electron density. For
structure, all H-atom ellipsoids are positive definite. The
largest differences between the classical and Hirshfeld
atomic refinement concern evidently the H-atom positions.
For instance, the P1–N11–H111 angle in the classical
PLATON [30] and Mercury [31] programs were used
for making the ORTEP and packing diagrams. COMP-
STRU [32] was used for the structure similarity
calculations.
structure
1
is 115.96° and that in the HAR
1
23

Synthesis and crystal structures of new phosphoric triamides: study of intermolecular…
Fig. 11 Up: dnorm Hirshfeld surface in two different orientations (left
and middle) and Hirshfeld surface mapped with shape index (right),
surrounded by neighboring molecules associated with close contacts
H…F/F…H (black dash lines, white areas) or p…p stacking, for
molecule P1 of 2. Down: Decomposed fingerprint plots and percent-
age contributions to the total HS for intermolecular contacts F…H/
H…F and C…C for molecule P1 of 2. The full fingerprint plot
appears as a grey shadow below each decomposed plot
3
2C), 25.57 (s, 2C), 27.71 (d, J(P,C) = 4.6 Hz, 2C), 30.76
Synthesis of phosphoric triamides 1 and 2
2
m, 6C), 54.72 (d, J(P,C) = 4.6 Hz, 2C), 112.55 (d,
(
2
2
,3,6-F –C H C(O)NHP(O)Cl was synthesized from the
2
J(F,C) = 21.3 Hz, 1C, CAr), 117.71 (m, 1C, CAr), 118.89
3
6
2
reaction of phosphorus pentachloride (16 mmol) and 2,3,6-
(m, 1C, CAr), 145.30 (m, 1C, CAr), 147.74 (m, 1C, CAr),
1
154.31 (d, J(F,C) = 249.7 Hz, 1C, CAr), 160.81 (s, 1C,
trifluorobenzamide (16 mmol) in dry CCl at 358 K (3 h)
4
3
1
1
under reflux condition and then the treatment of formic
acid (16 mmol) at ice bath temperature. For the preparation
C(O)) ppm;
298.4 K, 85% H
(376.47 MHz, DMSO-d
(s), - 138.16 (m), - 119.25 (m) ppm.
P{ H} NMR (161.97 MHz, DMSO-d ,
6
1
9
PO
4
): d = 11.69 (s) ppm; F NMR
, 296.5 K, CFCl ): d = - 142.53
3
of 1,
(
a
solution of 2,3,6-F –C H C(O)NHP(O)Cl
2
6
3
3
6
2
3
2 mmol) in 20 cm CH CN was added at 273 K to a
3
3
solution of N-methylcyclohexylamine (8 mmol) in 5 cm
0
0
00
N,N,N ,N -Tetraethyl-N -(2,3,6-trifluorobenzoyl)phosphoric
triamide (2, C H F N O P) Mp.: 126 °C; IR (KBr):
of the same solvent. After stirring for 4 h, the solvent was
evaporated and the product was washed with distilled
water. Compound 2 obtained in a similar procedure to 1 but
using diethylamine instead of N-methylcyclohexylamine.
Colorless single crystals, suitable for X-ray structural
analysis, were obtained at room temperature from a mix-
ture of CH OH/DMF/n-C H (3:1:1 v/v) for both 1 and 2.
1
5 23 3 3 2
mꢀ = 3061, 2976, 2935, 2876, 1695, 1633, 1492, 1473, 1385,
1
282, 1217, 1175, 1105, 1022, 947, 849, 829, 795, 719,
-1
41, 623, 559, 498 cm ; H NMR (400.13 MHz, DMSO-
1
6
3
d , 295.8 K, TMS): d = 1.06 (t, J(H,H) = 7.1 Hz, 12H,
6
4
CH ), 2.50–3.34 (m, 8H, 4CH ), 7.21 (m, 1H, Ar–H), 7.59
3 2
3
6 14
13
m, 1H, Ar–H), 9.77 (s, 1H, NH) ppm; C NMR
(
0
00
0
N,N -Dicyclohexyl-N -(2,3,6-trifluorobenzoyl)-N,N -
(100.62 MHz, DMSO-d , 298.5 K, TMS): d = 14.17 (d,
6
3
2
J(P,C) = 1.9 Hz, 4C), 39.13 (d, J(P,C) = 4.8 Hz, 4C),
dimethylphosphoric triamide (1, C H F N O P) Mp.:
72 °C; IR (KBr): mꢀ = 3047, 2935, 2858, 2781, 1670,
636, 1491, 1456, 1296, 1221, 1180, 1061, 1024, 972, 951,
2
1 31 3 3 2
2
112.53 (d, J(F,C) = 24.3 Hz, 1C, CAr), 117.72 (m, 1C,
1
1
8
CAr), 118.91 (m, 1C, CAr), 145.37 (m, 1C, CAr), 147.82 (m,
1
1C, CAr), 154.34 (d, J(F,C) = 245.8 Hz, 1C, CAr), 160.81
-
1
1
27, 720, 771, 571, 507, 468 cm
;
H
NMR
3
(s, 1C, C(O)) ppm; P{ H} NMR (161.97 MHz, DMSO-
1
1
(
400.13 MHz, DMSO-d , 297.5 K, TMS): d = 0.99–1.77
m, 20H), 2.54 (m, 6H), 3.33 (m, 2H), 7.21 (m, 1H, Ar–H),
1
.59 (m, 1H, Ar–H), 8.28 (s, 1H, NH) ppm; C NMR
6
1
9
(
d
6
, 296.4 K, 85% H
(376.47 MHz, DMSO-d
(s), - 138.01 (m), - 119.00 (m) ppm.
3
PO
4
): d = 10.76 (s) ppm; F NMR
3
7
6
, 295.5 K, CFCl ): d = - 142.57
3
(
100.62 MHz, DMSO-d , 298.4 K, TMS): d = 24.33 (s,
6
123

A. Tarahhomi, A. van der Lee
Fig. 12 Up: views of dnorm Hirshfeld surface for 3 generated for the
major disordered components in two orientations, surrounded by
neighboring molecules associated with close contacts O…H/H…O
(C–H…O hydrogen bonds, black dashed lines) as red spots on
surface; down: decomposed H…H and O…H/H…O FPs and related
percentage contribution to the total HS area shown in down
Tris(morpholin-4-yl) phosphine oxide (3) For the prepa-
ration of 3, a solution of morpholine (12 mmol) in 5 cm
fully optimized and characterized as true minima by the
absence of imaginary frequencies, but the calculations for
the analysis of the crystal structure and intermolecular
interactions were performed using the crystal geometry,
i.e., with possible imaginary frequencies. The C–H-bond
3
dry CH CN was added at 273 K to a solution of P(O)Cl
3
3
3
(
2 mmol) in 10 cm of the same solvent. After stirring for
h, the precipitated amine hydrochloride salt (OC H
4
4
8-
˚
lengths were renormalized to their neutron value of 1.08 A,
˚
while O–H and N–H bonds were fixed at 1.00 A. Lattice
NHÁHCl) was filtered off and the acetonitrile solution of
[
OH C N] P(O) was used in a reaction with Cu(NO )
3 2-
8
4
3
4
H O in CH OH under reflux. Single crystals of 3 were
3
and intermolecular interaction energies were calculated
using the PIXEL module in the Coulomb London Pauli
(CLP) computer program package [34]. The program
PIXEL provides the advantage of partitioning the total
interaction energy for the different molecular pairs into the
corresponding coulombic, polarization, dispersion, and
repulsion components, respectively, which reveals how
molecules interact in crystals. Coulombic and linear-po-
larization terms are calculated by classical formulae [35]
using charge densities and their electric fields, whereas the
dispersion and repulsion terms are evaluated by the London
approach [36] and Pauli spin avoidance [37], respectively,
where the former term is due to electron correlation and the
2
obtained fortuitously from slow evaporation of the filtered
solution of the mentioned reaction at room temperature.
M.p.: 184–186 °C (187–188 °C [19]); IR (KBr): mꢀ = 2965,
2
1
4
847, 1456, 1367, 1325, 1296, 1258, 1207, 1130, 1115,
090, 1024, 956, 918, 847, 733, 675, 621, 571, 518,
-
1
82 cm
.
Computational calculations
Optimization of the crystal structures was performed at
MP2 level of theory at 6-31G(d,p) basis set using Gaus-
sian09 [33]. The structures for the studied molecules were
1
23

Synthesis and crystal structures of new phosphoric triamides: study of intermolecular…
latter term is appraised depending on the amount of overlap
between proximal charge densities [17]. Selected molecu-
lar pairs were further analyzed using the Atom In Molecule
Acknowledgements Support of this investigation by Semnan
University is gratefully acknowledged.
(
AIM) theory (at the MP2/6-31G(d,p) level) which is a
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