The first C(O)NHP(O)-based phosphoric triamide structure with an N?H···π hydrogen bonding: A combination of X-ray crystallography and theoretical study to evaluate the strength of hydrogen bonds

Article abstract of DOI:10.1080/10426507.2017.1295960

The hydrogen bond pattern of N-(4-methoxybenzoyl)-N′,N″-bis(4-methylbenzyl)-phosphoric triamide, C24H28N3O3P, (I), was investigated. In the crystal structure, the molecules are aggregated through NCP–H···O═P andNP–H···O═C hydrogen bonds in a one-dimensional arrangement parallel to the c axis (NCP is the nitrogen atom in the C(O)NHP(O) segment and NP stands for the two other nitrogen atoms bonded to the P atom). There is also a novel NP–H···π hydrogen bond in the crystal which extends the aggregation of the molecules to a two-dimensional array parallel to the bc plane. A Cambridge Structural Database (CSD, version 5.37, Feb 2016) analysis shows that the N–H···π hydrogen bond was not observed in any of 156 [RC(O)NH]P(O)[NR1R2]2 (R1 ≠ H, R₂ = H or ≠ H) phosphoric triamide structures reported so far. The theoretical calculations at the B3LYP/6-311G?? level of theory (DFT, AIM, and NBO) were performed to evaluate the strengths of NCP–H···O═P, NP–H···O═C and N_P–H···π hydrogen bonds, considering two-aggregate molecular assemblies containing these hydrogen bonds. The calculations on the title compound suggest that the intermolecular N_CP–H···O═P hydrogen bond is stronger than N_P–H···O═C and N_P–H···π interactions. The hydrogen bond strength was investigated by NBO, topological analysis, geometry calculation, Hirshfeld surface analysis and experimental spectroscopic results, which are in agreement with each other.

Full text of DOI:10.1080/10426507.2017.1295960

Phosphorus, Sulfur, and Silicon and the Related Elements
ISSN: 1042-6507 (Print) 1563-5325 (Online) Journal homepage: http://www.tandfonline.com/loi/gpss20
The first C(O)NHP(O)-based phosphoric triamide
structure with an N—H···π hydrogen bonding:
a combination of X-ray crystallography and
theoretical study to evaluate the strength of
hydrogen bonds
Maryam Taherzadeh, Mahrdad Pourayoubi, Raheleh Afzali & Marek Nečas
To cite this article: Maryam Taherzadeh, Mahrdad Pourayoubi, Raheleh Afzali & Marek
Nečas (2017): The first C(O)NHP(O)-based phosphoric triamide structure with an N—H···π
hydrogen bonding: a combination of X-ray crystallography and theoretical study to evaluate the
strength of hydrogen bonds, Phosphorus, Sulfur, and Silicon and the Related Elements, DOI:
10.1080/10426507.2017.1295960
To link to this article: http://dx.doi.org/10.1080/10426507.2017.1295960
Accepted author version posted online: 21
Feb 2017.
Submit your article to this journal
Article views: 2
View related articles
View Crossmark data
Full Terms & Conditions of access and use can be found at
http://www.tandfonline.com/action/journalInformation?journalCode=gpss20
Download by: [University of Newcastle, Australia]
Date: 05 March 2017, At: 23:56

ACCEPTED MANUSCRIPT
The first C(O)NHP(O)-based phosphoric triamide structure with an N—H∙∙∙π hydrogen
bonding: a combination of X-ray crystallography and theoretical study to evaluate the
strength of hydrogen bonds
Maryam Taherzadeha, Mahrdad Pourayoubia,*, Raheleh Afzalia and Marek Nečasb,c
aDepartment of Chemistry, Faculty of Sciences, Ferdowsi University of Mashhad, Mashhad, Iran
bDepartment of Chemistry, Masaryk University, Kotlarska 2, 61137 Brno, Czech Republic
cCEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 62500
Brno, Czech Republic
*Correspondence e-mail: pourayoubi@um.ac.ir
Abstract
The hydrogen bond pattern of N,N'-bis(4-methylbenzyl)-N"-(4-methoxybenzoyl)-phosphoric
triamide, C24H28N3O3P, (I), was investigated. In the crystal structure, the molecules are
aggregated through NCP―H∙∙∙O═P and NP―H∙∙∙O═C hydrogen bonds in a one-dimensional
arrangement parallel to the c axis (NCP is the nitrogen atom in the C(O)NHP(O) segment and NP
stands for the two other nitrogen atoms bonded to the P atom). There is also a novel NP—H∙∙∙π
hydrogen bond in the crystal which extends the aggregation of the molecules to a two-
dimensional array parallel to the bc plane. A Cambridge Structural Database (CSD, version 5.37,
Feb 2016) analysis shows that the N―H∙∙∙π hydrogen bond was not observed in any of 156
[RC(O)NH]P(O)[NR1R2]2 (R1 ≠ H, R2 = H or ≠ H) phosphoric triamide structures reported so far.
The theoretical calculations at the B3LYP/6-31G** level of theory (DFT, AIM, and NBO) were
performed to evaluate the strengths of NCP―H∙∙∙O═P, NP―H∙∙∙O═C and NP―H∙∙∙π hydrogen
1
ACCEPTED MANUSCRIPT

ACCEPTED MANUSCRIPT
bonds, considering two-aggregate molecular assemblies containing these hydrogen bonds. The
calculations on the title compound suggest that the intermolecular NCP―H∙∙∙O═P hydrogen bond
is stronger than NP―H∙∙∙O═C and NP―H∙∙∙π interactions. The hydrogen bond strength was
investigated by NBO, topological analysis, geometry calculation, Hirshfeld surface analysis and
experimental spectroscopic results, which are in agreement with each other.
Keywords
Phosphoric triamide; X-ray diffraction; N—H∙∙∙O hydrogen bond; N—H∙∙∙π hydrogen bond;
DFT calculation; Hirshfeld surface analysis
2
ACCEPTED MANUSCRIPT

ACCEPTED MANUSCRIPT
INTRODUCTION
The hydrogen bond is the most versatile intermolecular interaction responsible for molecular
aggregation in the material world.1–3 Conventionally, intermolecular interaction N—H∙∙∙O occurs
in a molecule containing N—H functional group as a donor group and O atom as an acceptor
group; such interaction is extensively discussed in the area of crystal engineering of phosphoric
triamide compounds.4–10
The N—H donor group is placed along the free electron pair of the oxygen atom, offering an
efficient force for constructing various predictable supramolecular structures (for example
secondary structures such as dimers and polymers) showing high directionality and strength.11
In some recently published papers, the hydrogen bond patterns and the motifs constructed
were described in detail8,12,13 and the properties such as donor directionality,14 differences in the
strengths of N—H∙∙∙O═P and N—H∙∙∙O═C hydrogen bonds and their effects on the N—H
stretching frequencies were discussed.9 Furthermore, for the compounds including higher
numbers of H-donor sites with respect to the lower number(s) of H-acceptor site(s), the double
hydrogen bond acceptor capability of the P═O group in forming P═O(∙∙∙H)(∙∙∙H) grouping were
discussed and the competition between different acceptor sites with different strengths of
acceptor capabilities were considered.15
In recent years, the focus has been extended towards the understanding of weak
intermolecular interactions in the crystal design, for example C—H∙∙∙X (X = O, N, halogen
atoms, unsaturated segments), O—H∙∙∙π and N—H∙∙∙π.16–20 There are many
[RC(O)NH]P(O)[NR1R2]2 (R1 ≠ H, R2 = H or ≠ H) phosphoric triamide structures including C—
H∙∙∙X interaction,8,21,22 but so far no N—H∙∙∙π hydrogen bond was seen in any of 156 structures
3
ACCEPTED MANUSCRIPT

ACCEPTED MANUSCRIPT
deposited in the Cambridge Structural Database (CSD; version 5.37,Feb 2016). It should be
noted that only in a limited number of these compounds C═O∙∙∙π interactions can be seen.23
In the present work we report on the synthesis, spectroscopic characterization and X-ray
crystallography of [(4-CH3O)C6H4C(O)NH]P(O)[NHCH2C6H4(4-CH3)]2 (I) (Figure 1), namely
N,N'-bis(4-methylbenzyl)-N"-(4-methoxybenzoyl)-phosphoric triamide as the first example of a
crystalline phosphoric triamide showing the NP—H∙∙∙π hydrogen bond. Furthermore, the strength
of this interaction was compared with the strengths of the two commonly occuring hydrogen
bonds NCP—H∙∙∙O═P and NP—H∙∙∙O═C by means of DFT calculations. The intermolecular
interactions were further studied by Hirshfeld surface analysis. In our discussion, NCP is the
nitrogen atom in the C(O)NHP(O) segment and NP stands for the two other nitrogen atoms
bonded to the phosphorus atom.
RESULTS AND DISCUSSION
Description of the crystal structure
The asymmetric unit of (I) contains one complete molecule, as shown in Figure 2. The crystal
data and the refinement parameters are listed in Table 1. The P—NCP bond is significantly longer
than the two P—NP bonds (Table 2). The NCP—H adopts a syn orientation with respect to the
P═O group, while the two NP—H units adopt different conformations with respect to the P═O
group (as anti and gauche). The phosphorus atom has a distorted tetrahedral configuration (Table
2). The bond-angle sums at the N atoms (P—N—C + C—N—H + H—N—P) of 359.4°(13) N1,
355.9°(13) N2 and 359.8°(12) N3 confirm the sp2 character of the nitrogen atoms bonded to the
phosphorus atom. The criterion for proposing the sp2 hybridization is in accordance to a previous
work for amides, suggesting the sp2 character for bond-angle sums ≥ 352.5°.24
4
ACCEPTED MANUSCRIPT

ACCEPTED MANUSCRIPT
In the crystal structure, adjacent molecules are linked via NCP—H∙∙∙O═P and NP—H∙∙∙O═C
( )
hydrogen bonds, building alternating and ( ) rings, propagated in a linear
arrangement along the c axis (for graph-set notation, see refs. 25 and 26). The NP―H unit which
does not take part in the NP—H∙∙∙O hydrogen bond is involved in the NP—H∙∙∙π interaction
(Figure 3). According to previous work classification,20,27 the N—H∙∙∙π interaction in the
structure of I is considered as one-center proton donor and six-center proton acceptor in a T-
shape arrangement, in which the N3—H vector nearly points towards the center of C18–C23
six–membered ring.
Positively charged (δ(+)) NP—H hydrogen of a (4-CH3)C6H4CH2NH segment in the
phosphoramide molecule is preferentially located within 2.43(2) Å of the ring centroid of the
same but is symmetrically different from such a group of next phosphoramide molecule, where it
makes van der Waals contact with the δ(-) π–electrons and avoids the δ (+) ring edge.
For comparison, a survey of the Cambridge Structural Database (CSD)28,29 was performed for
[RC(O)NH]P(O)[NHR1]2 structures. In all of the acyclic [RC(O)NH]P(O)[NHR1]2 structures in
the CSD, both Np–H have an anti orientation with respect to the P═O group, different from two
NP–H groups in the structure of I. The gauche orientation of N3—H unit and a suitable
conformation of the C18–C23 six–membered ring leads to the formation of NP—H∙∙∙π hydrogen
bond. Another driving force for such an interaction is the presence of electron-rich 4-
methylphenyl system. While such interaction is novel for [RC(O)NH]P(O)[NHR1]2 structures, it
is known for proteins, based on the survey published in 2001.30 The geometries of hydrogen
bonds are listed in Table 3.
5
ACCEPTED MANUSCRIPT

ACCEPTED MANUSCRIPT
Hirshfeld surface analysis and fingerprint plots
The Hirshfeld surface analysis, which uses three-dimension (3D) surfaces functions, as well as
two-dimension (2D) fingerprint plots,31,32 is a very useful graphical tool for identification and
understanding of intermolecular interactions within a crystal structure. The Hirshfeld surfaces
mapped with dnorm and corresponding shape index associated 2D fingerprint plots of I was
generated using the Crystal Explorer software version 3.1,33 using the structure file in the CIF
format as the input.
Two large red areas can be noticed (labels 1 and 2 in Figure 4), which correspond to two N–
H···O hydrogen bonds noted in the crystal structure section. According to Table 3, the difference
between hydrogen bond strengths of NCP—H∙∙∙O═P and NP—H∙∙∙O═C is very small, reflecting
in a slightly difference between the intensities of the red spots. The other large red spot, with
label 5 (Figure 4), is in accordance with N—H∙∙∙π hydrogen bond. Less color intensity of this red
area shows that the N—H∙∙∙π hydrogen bond is weaker than NCP—H∙∙∙O═P and NP—H∙∙∙O═C
hydrogen bonds. Several small and pale red spots in the related Hirshfeld surfaces are observed,
which correspond to weak C3-H3A∙∙∙O3=P1 (label 3), C24-H24A∙∙∙O3=P1 (label 4) and C7-
H7∙∙∙C10 (label 6) interactions (Figure 4).
In order to obtain more information on the crystal packing, the two-dimensional fingerprint
plots were also considered (Figure 5). The full plot was also divided to the figures illustrating
partial interactions observed in the crystal. According to divided finger prints, the major
frequently occurring contacts are the H···H van der Waals forces and then the C···H / H···C
contacts with the contribution portions of 57.9 % and 24.7 %, respectively. The other contacts in
the crystal are O···H / H···O (13.8 %) and N···H / H···N (1.1 %). Furthermore, in the fingerprint
6
ACCEPTED MANUSCRIPT

ACCEPTED MANUSCRIPT
plot, the H∙∙∙O interactions develop two sharp and symmetric spikes that are indicative of
stronger interactions received by oxygen atoms.
Spectral studies
1
In the H NMR spectrum (in DMSO-d6), the signals at 2.22 and 3.79 ppm correspond to the
methyl and methoxy protons. The multiplet signal at 3.98 ppm is assigned to the CH2 protons
3
and the ―dd‖ signal at 4.89 ppm (2J(P,H) = 16.6 Hz, J(H,H) = 7.1 Hz) is related to the Np—H
proton. The aromatic protons display doublets at 6.96, 7.03, 7.21 and 7.92 ppm (3J(H,H) = 8.5,
7.8, 7.7 and 8.5 Hz, respectively). The NCP—H proton appears as a broad signal at 8.32 ppm. The
31P NMR signal is observed at 9.49 ppm.
According to Figure 6, the absorption bands centered at 3187 and 3311 cm–1 are assigned to
the (NH) stretching vibrations for the NH units participating in NCP—H∙∙∙O═P and Np—
H∙∙∙O═C hydrogen bonds, respectively. The absorption band observed at 3390 cm–1 belongs to
the other NH unit involving in a weaker NP—H∙∙∙π hydrogen bond, which appears as sharper
band with respect to the two other ones. This is similar to what was previously reported in
literature for wider band for N—H cooperating in a stronger hydrogen bond.34 The C═O and
P═O stretching frequencies appear at 1648 cm–1 and 1255 cm–1, respectively.
The ultraviolet (UV) absorption spectra were also recorded for (I) (Figure 7) as well as for
the starting compounds 4-methylbenzylamine and 4-methoxybenzamide for comparison.
According to Figure 7, for (I) and also for the amine one of the absorption bands appears at 257
nm, while the similar band appears at 256 nm for amide, which is attributed to π→π* transition.
The other bands at lower wave lengths with a maximum at 207 nm (for (I)) and 208 nm (for 4-
methoxybenzamide) are assigned to C═O segment transitions. So, due to the little difference
7
ACCEPTED MANUSCRIPT

ACCEPTED MANUSCRIPT
between some observed values, UV spectroscopy is not a good choice for the investigation of
hydrogen bonding. A similar conclusion was previously derived from the investigation of O—
H∙∙∙N and O—H∙∙∙π hydrogen bonding with aromatic rings as acceptors by different
spectroscopic methods.35
Theoretical study of molecular structure
In order to investigate hydrogen bond strength by DFT method, compound (I) was studied as a
hydrogen-bonded dimer. This strategy is of benefit as the effects of different types of hydrogen
bonds found in the crystal packing are considered separately. The optimized dimeric structures
were constructed by using the solid state structure (CIF file) as a starting point. After the
calculation was performed on the monomer in the first stage, the dimers formed through NCP—
H∙∙∙O═P, NP—H∙∙∙O═C and NP—H∙∙∙π hydrogen bonds were checked in the next stage (Figure
8).
Selected fully optimized geometrical parameters of compound (I) and its dimers constructed
with NCP—H∙∙∙O═P, NP—H∙∙∙O═C, and NP—H∙∙∙π hydrogen bonds are collected in Table 2.
According to this table, the theoretical results are in good agreement with experimental data,
nearly in the experimental error range. The only significant deviation is observed for the N–H
bonds. It should be noted that the positions of nitrogen-bonded hydrogen atoms obtained from X-
ray crystallography can be located more accurately by using Hirshfeld atom refinement (HAR)
with the same accuracy as neutron normalization.36 After doing HAR, the N–H bonds length
change to 1.009 Å. This variation could be interpreted by considering of a double minimum type
potential function for the movement of the proton. In such a potential surface, the position of the
proton is not exactly at the theoretical minima since it lies at the zero point energy, ZPE, and, by
8
ACCEPTED MANUSCRIPT

ACCEPTED MANUSCRIPT
considering the anharmonicity of the potential function, the N–H bond distance should be longer
than that predicted by the theory.
As Table 2 shows, the calculated P═O bond length in the monomer is significantly shorter
than in the dimer structure formed through a pair of NCP—H∙∙∙O═P hydrogen bonds. The bond-
valence calculations were performed for the P═O segment using the equation Sij = exp[(R0 –
Rij)/bij], where Sij is the bond valence portion between atoms i and j (here, P and O), R0 is the
standard value of the bond distance for these atoms, Rij is the actual bond distance obtained from
chemical calculation, and bij is a constant.37,38 Such a calculation provides bond-valence (BV)
values of 1.41 valence units (v.u.) for the P═O of the monomer and 1.36 v.u. for the dimer (Rij is
1.489 Å for the monomer and 1.502 Å for the dimer as given in Table 2, R0 = 1.617 Å and bij =
0.37). Decrease of the bond-valence (BV) value refers to the hydrogen bond formed.
By comparison of the N—H bond lengths, which are involved in hydrogen bonding, it is
obvious that this bond in NCP—H∙∙∙O═P is longer than the others. Thus, the following trend in
hydrogen bond strength is obtained: NCP—H∙∙∙O═P > NP—H∙∙∙O═C > NP—H∙∙∙π. The results of
AIM and NBO studies confirm this conclusion.
AIM and topological analysis
The topological parameters such as total electron density, (r), and its corresponding Laplacian,
2(r), which are analyzed by ―Atoms in Molecules‖ (AIM) of Bader theory, point out that a
critical point exists between two chemically bonded atoms. The calculated total electronic
density and its corresponding Laplacian at the bond critical point, potential electron energy
density (V(r)), kinetic electron energy density (G(r)), the ratio of G(r)/V(r) at bond critical point,
and intermolecular hydrogen bond (IHB) energy of the three dimer structures of [(4-
9
ACCEPTED MANUSCRIPT

ACCEPTED MANUSCRIPT
CH3O)C6H4C(O)NH]P(O)[NHCH2C6H4(4-CH3)]2 with different hydrogen bonds are given and
compared in Table 4. According to this table, the total electronic density, (r), is positive in all
the mentioned dimers, which is characteristic of closed shell interactions, and also the –G(r)/V(r)
values in all cases are near to unit and partly covalent nature of hydrogen bonds can be
concluded. According to previous work,39 the hydrogen bond strength can be classified, as weak
strength hydrogen bonded in this system (weak hydrogen bonds have EI < 12.0 kcal/mol and
show 2(r) > 0). It is obvious from Table 4 that the intermolecular hydrogen bonding strength
follows this trend: NCP—H∙∙∙O═P > NP—H∙∙∙O═C > NP—H∙∙∙π. The calculated total electronic
density and its corresponding Laplacian at the bond critical point also follow this trend.
Electron delocalization
Delocalization of electron density between occupied Lewis type (bond or lone pair) NBO
orbitals and formally unoccupied (antibonding or Rydberg) non-Lewis NBO orbitals corresponds
to a stabilizing donor-acceptor interaction. The energy of these interactions can be estimated by
the second order perturbation theory.40 Table 5 lists some of the important calculated second
order interaction energies E(2) between the donor–acceptor orbitals in the three mentioned dimer
structures. According to this table, the total second order energy in NCP—H∙∙∙O═P > NP—
H∙∙∙O═C > NP—H∙∙∙π, which confirms the higher hydrogen bonding strength in NCP—H∙∙∙O═P.
Conclusion
We have shown on the basis of a CSD analysis of phosphoric triamide compounds that while
N—H∙∙∙O hydrogen bonding is common, N—H∙∙∙π hydrogen bonding does not occur. [(4-
CH3O)C6H4C(O)NH]P(O)[NHCH2C6H4(4-CH3)]2 is the first representative of a phosphoric
triamide, in which N—H∙∙∙π hydrogen bonding can be observed (in addition to N—H∙∙∙O
10
ACCEPTED MANUSCRIPT

ACCEPTED MANUSCRIPT
hydrogen bonding). The proton acceptor groups comprise one center (NCP—H∙∙∙O═P and NP—
H∙∙∙O═C) and six centers (NP—H∙∙∙π), which is a distinguishing feature for both types of
interactions. So, in the crystal structure, each component of the mentioned compound is
connected to other three molecules via intermolecular NCP—H∙∙∙O═P, NP—H∙∙∙O═C, and NP—
H∙∙∙π hydrogen bonds. Besides, the investigation revealed that the oxygen is a stronger Lewis
base center than the π-electrons of the phenyl ring. The structural parameters, NBO and AIM
analyses show a consistent trend of intermolecular hydrogen bond (IHB) strength for the dimers,
which is NCP—H∙∙∙O═P > NP—H∙∙∙O═C > NP—H∙∙∙π. Investigation of the Hirshfeld surface
analysis confirm this matter.
Experimental
Synthesis of [(4-CH3O)C6H4C(O)NH]P(O)[NHCH2C6H4(4-CH3)]2
According to Scheme 2, for the synthesis of (I), at first [(4-CH3O)C6H4C(O)NH]P(O)[Cl]2
reagent was synthesized. The compound [(4-CH3O)C6H4C(O)NH]P(O)[Cl]2 was prepared by
refluxing phosphorus pentachloride and (4-CH3O)C6H4C(O)NH2 in an equimolar ratio in dry
CCl4 for 3 h. Then the reaction mixture was cooled with an ice-bath and the equimolar amount of
formic acid was added drop-wise by means of a syringe into the cold solution. The resulting
colorless solution containing a white precipitate was stirred at 25 °C for 2 h. After completion of
the reaction (monitored by appearance of the evolution of gas bubbles through an oil blubberer),
the stirring was stopped and then the solvent was removed under reduced pressure and trapped in
a liquid nitrogen-cooled trap. The solid obtained was used for the synthesis of [(4-
CH3O)C6H4C(O)NH]P(O)[NHCH2C6H4(4-CH3)]2.
11
ACCEPTED MANUSCRIPT

ACCEPTED MANUSCRIPT
A solution of 4-methylbenzylamine (10 mmol) in CH2Cl2 (25 mL) was added drop-wise to a
solution of [(4-OCH3)C6H4C(O)NH]P(O)[Cl]2 (2.5 mmol) in the same solvent (25 mL) at 273 K.
After 4 h stirring at ice bath temperature, the procedure was stopped and the mixture transferred
to a beaker and kept at room temperature for a few days to remove the solvent. The solid
obtained was washed with distilled water to remove the [NH3CH2C6H4(4-CH3)]Cl by-product.
Suitable single crystals were obtained from a solution of the synthesized compound in
CH3OH/CHCl3 (1 : 2 v/v) at room temperature after a few days. Anal. Calcd. for (C24H28N3O3P):
C: 65.90; H: 6.41; N: 9.61; Found: C: 64.20; H: 6.36; N: 9.49 %. 1H NMR (DMSO-d6): δ = 2.23
(d, 2J(H,H) = 8.4 Hz, 6H, CH3), 3.78 (d, 2J(H,H) = 5.9 Hz, 3H, OCH3), 3.99 (dd, 3J(H,H) = 10.9
3
2
3
Hz, J(P,H) = 6.4 Hz, 4H, CH2), 4.89 (dd, J(P,H) = 16.6 Hz, J(H,H) = 7.1 Hz, 2H, NH), 6.96
3
3
3
(d, J(H,H) = 8.5 Hz, Ar–H), 7.03 (d, J(H,H) = 7.8 Hz, Ar–H), 7.21 (d, J(H,H) = 7.7 Hz, Ar–
3
31
H), 7.92 ppm (d, J(H,H) = 8.5 Hz, Ar–H), 8.32 (s, 1H, NCPH). P NMR (DMSO-d6): δ = 9.5
(s). IR (cm–1): 3390, 3311, 3187, 3008, 2915, 2660, 1648, 1605, 1576, 1516, 1433, 1409, 1310,
1255, 1187, 1102, 1057, 1032, 899, 849, 805, 773, 694, 557, 541, 474.
Data collection and structure refinement
The diffraction data were collected with a Rigaku MicroMax-007 HF rotating anode four-circle
CCD diffractometer with Mo-Kα radiation. The data were processed using Rigaku
CrystalClear.41 The structure was solved by Direct Methods and then refined by full-matrix least-
squares method on F2. The SHELXTL and WinGX software packages were used for the
structure solution and refinement.42,43
Analytical studies
12
ACCEPTED MANUSCRIPT

ACCEPTED MANUSCRIPT
13
31
1H, C and P NMR spectra were recorded with a FT-NMR Bruker Avance 300 spectrometer.
1H and 13C NMR spectra were referenced using the solvent DMSO-d6 resonances (2.50 and
1
39.52 ppm for H and 13C, respectively) and the 31P NMR spectrum was calibrated using
1
―absolute referencing‖ from the H spectrum. The IR spectrum was recorded with a Thermo
Nicolet Avatar 370 FTIR spectrometer using a KBr pellet. Elemental analysis (C, H and N) was
performed with a Thermo Finnigan Flash 1112EA elemental analyzer. An Agilent model 8453
UV–visible spectrophotometer was employed to obtain the UV spectrum.
Method of theoretical analysis
All quantum calculations have been performed using Gaussian 09W44, NBO 5.045 and
AIM200046 software programs. The dimer structures of different hydrogen bonds of [(4-
CH3O)C6H4C(O)NH]P(O)[NHCH2C6H4(4-CH3)]2 have been optimized at the B3LYP47,48 level,
using 6-31G** basis set. AIM 2000 software46 was applied to obtain electron density at
hydrogen bond critical points according to Bader’s atoms in molecules (AIM) theory49 at the
B3LYP/6-31G** level of theory.
Acknowledgement
This research has been financially supported by the Ministry of Education, Youth and Sports of
the Czech Republic under the project CEITEC 2020 (LQ1601). We acknowledge the CF X-ray
diffraction and Bio-SAXS supported by the CIISB research infrastructure (LM2015043 funded
by MEYS CR) for their support with obtaining scientific data presented in this paper. The partial
support of this work by Ferdowsi University of Mashhad is gratefully acknowledged.
13
ACCEPTED MANUSCRIPT

ACCEPTED MANUSCRIPT
REFERENCES
1. Allen, F. H.; Motherwell, W. D. S. Acta Cryst. B 2002, 58, 407–422.
2. Allen, F. H.; Taylor, R. Chem. Soc. Rev. 2004, 33, 463–475.
3. McKenzie, J.; Feeder, N.; Hunter, C. A. CrystEngComm 2016, 18, 394–397.
4. Chivers, T.; Krahn, M.; Schatte, G.; Parvez, M. Inorg. Chem. 2003, 42, 3994–4005.
5. Gholivand, K.; Mahzouni, H. R. Acta Cryst. B 2011, 67, 238–243.
6. Gholivand, K.; Mostaanzadeh, H.; Koval, T.; Dusek, M.; Erben, M. F.; Della Védova, C. O.
Acta Cryst. B 2009, 65, 502–508.
7. Gholivand, K.; Mostaanzadeh, H.; Koval, T.; Dusek, M.; Erben, M. F.; Stoeckli-Evans, H.;
Della Védova, C. O. Acta Cryst. B 2010, 66, 441–450.
8. Pourayoubi, M.; Toghraee, M.; Zhu, J.; Dušek, M.; Bereciartua, P. J.; Eigner, V.
CrystEngComm 2014, 16, 10870–10887.
9. Pourayoubi, M.; Izadyar, M.; Elahi, B.; Parvez, M. J. Mol. Struct. 2013, 1034, 354–362.
10. Keikha, M.; Pourayoubi, M.; Tarahhomi, A.; van der Lee, A. Acta Cryst. C 2016, 72, 251–
259.
11. Ahmed, M.; Jelsch, C.; Guillot, B.; Lecomte, C.; Domagała, S. Cryst. Growth Des. 2013, 13,
315−325.
12. Pourayoubi, M.; Tarahhomi, A.; Saneei, A.; Rheingold, A. L.; Golen, J. A. Acta Cryst. C
2011, 67, 265–272.
13. Toghraee, M.; Pourayoubi, M.; Divjakovic, V. Polyhedron 2011, 30, 1680–1690.
14. Pourayoubi, M.; Toghraee, M.; Divjakovic, V.; van der Lee, A.; Mancilla Percino, T.; Leyva
Ramírez, M. A.; Saneei, A. Acta Cryst. B 2013, 69, 184–194.
14
ACCEPTED MANUSCRIPT

ACCEPTED MANUSCRIPT
15. Pourayoubi, M.; Nečas, M.; Negari, M. Acta Cryst. C 2012, 68, 51–56.
16. Isozaki, T.; Tsutsumi, Y-I.; Suzuki, T.; Ichimura, T. Chem. Phys. Lett. 2010, 495, 175–178.
17. Malathy Sony, S. M.; Ponnuswamy, M. N. Crystal Growth Des. 2006, 16, 736–742.
18. Paytakov, G.; Dinadayalane, T.; Leszczynski, J. J. Phys. Chem. A 2015, 119, 1190–1200.
19. Frontera, A.; Garau, C.; Quiñonero, D.; Ballester, P.; Costa, A.; Deyà, P. M. Org. Lett. 2003,
5, 1135–1138.
20. Domagała, M.; Grabowski, S. J. Chem. Phys. 2009, 363, 42–48.
21. Rebrova, O. N.; Byushkin, V. N.; Malinovskii, T. I.; Protsenko, L. D.; Dneprova, T. N. Dokl.
Akad. Nauk SSSR (Russ.) (Proc. Nat. Acad. Sci. USSR) 1982, 266, 1391.
22. Tarahhomi, A.; Pourayoubi, M.; Rheingold, A. L.; Golen, J. A. Acta Cryst. E 2011, 67, 2643.
23. Rostami Chaijan, M.; Pourayoubi, M.; Nečas, M.; Damodaran, K. Phosphorus, Sulfur,
Silicon Relat. Elem. 2015, 190, 911–917.
24. Allen, F. H.; Bruno, I. J. Acta Cryst. B, 2010, 66, 380–386.
25. Etter, M. C.; Macdonald, J. C. Acta Cryst. B 1990, 46, 256–262.
26. Bernstein, J.; Davis, R. E.; Shimoni, L.; Chang, N.-L. Angew. Chem. Int. Ed. Engl. 1995, 34,
1555–1573.
27. Grabowski, S. J. J. Phys. Chem. A 2007, 111, 3387–3393.
28. Görbitz, C. H. Acta Cryst B 2016, 72, 167–168.
29. Groom, C. R.; Bruno, I. J.; Lightfoot, M. P.; Ward, S. C. Acta Cryst. B, 2016, 72, 171–179.
30. Steiner, T.; Koellner, G. J. Mol. Biol. 2001, 305, 535–557.
31. McKinnon, J. J.; Jayatilaka, D.; Spackman, M. A. Chem. Commun. 2007, 3814–3816.
32. Spackman, M. A.; McKinnon, J. J. CrystEngComm 2002, 4, 378–392.
15
ACCEPTED MANUSCRIPT

ACCEPTED MANUSCRIPT
33. Wolff, S. K.; Grimwood, D. J.; McKinnon, J. J.; Turner, M. J.; Jayatilaka, D.; Spackman, M.
A. 2007, Crystal Explorer, University of Western Australia, Australia.
34. Gubina, K. E.; Amirkhanov, V. M. Z. Naturforsch. 2000, 55b, 1015–1019.
35. Zhao, H.; Chang, J.; Du, L. Comput. Theor. Chem. 2016, 1084, 126–132.
36. Woińska, M.; Grabowsky, S.; Dominiak, P. M.; Woźniak, K.; Jayatilaka, D. Sci. Adv. 2016,
2, doi: 10.1126/sciadv.1600192.
37. Brown, I. D.; Altermatt, D. Acta Cryst. B 1985, 41, 244–247.
38. http://www.iucr.org/resources/data/datasets/bondvalence- parameters.
39. Rozas, I.; Alkorta, I.; Elguero, J. J. Am. Chem. Soc. 2000, 11154–11161.
40. Reed, A. E.; Curtiss, L. A.; Weinhold, F. Chem. Rev. 1988, 88, 899–926.
41. Rigaku, CrystalClear-SM Expert, Version 2.0, 2011. Rigaku Americas Corporation, The
Woodlands, Texas, USA, and Rigaku Corporation, Tokyo, Japan, 2014.
42. Sheldrick, G. M. Acta Cryst. A 2008, 68, 112–122.
43. Farrugia, L. J. J. Appl. Cryst. 2012, 45, 849–854.
44. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J.
R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. A.; Nakatsuji, H.; Caricato, M.; Li,
X.; Hratchian, H. P.; Izmaylov, A. F.; Bloino, J.; Zheng, G.; Sonnenberg, J. L.; Hada, M.;
Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao,
O.; Nakai, H.; Vreven, T.; Montgomery Jr., J. A.; Peralta, J. E.; Ogliaro, F.; Bearpark, M.;
Heyd, J. J.; Brothers, E.; Kudin, K. N.; Staroverov, V. N.; Kobayashi, R.; Normand, J.;
Raghavachari, K.; Rendell, A.; Burant, J. C.; Iyengar, S. S.; Tomasi, J.; Cossi, M.; Rega, N.;
Millam, J. M.; Klene, M.; Knox, J. E.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.;
16
ACCEPTED MANUSCRIPT

ACCEPTED MANUSCRIPT
Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.;
Ochterski, J. W.; Martin, R. L.; Morokuma, K.; Zakrzewski, V. G.; Voth, G. A.; Salvador, P.;
Dannenberg, J. J.; Dapprich, S.; Daniels, A. D.; Farkas, O.; Foresman, J. B.; Ortiz, J. V.;
Cioslowski, J.; Fox, D. J. Gaussian 09, Revision A. 02, Gaussian Inc., Wallingford, CT,
2009.
45. Glendening, E. D.; Badenhoop, J. K.; Reed, A. E.; Carpenter, J. E.; Bohmann, J. A.; Morales,
C. M.; Weinhold, F. Theoretical Chemistry Institute, University of Wisconsin, Madison, WI,
2001.
46. Biegler-King, F. W.; Schoenbohm, J.; Bayles, D. AIM2000: a program to analyze and
visualize atoms in molecules, J. Comp. Chem. 2001, 22, 545–559.
47. Becke, A. D. Density-Functional Thermochemistry. III. The Role of Exact Exchange, J.
Chem. Phys. 1993, 98, 5648–5652.
48. Lee, C.; Yang, W.; Parr, R. G. Development of the Colle-Salvetti correlation energy formula
into a functional of the electron density, Phys. Rev. B 1988, 37, 785–789.
49. Bader, R. W. F. Atoms in Molecules. A Quantum Theory, Oxford University Press, New
York, 1990.
17
ACCEPTED MANUSCRIPT

ACCEPTED MANUSCRIPT
Table 1 Crystal data and structure refinement of [(4-CH3O)C6H4C(O)NH]P(O)[NHCH2C6H4(4-
CH3)]2 (I).
Empirical formula
Formula weight
C24H28N3O3P
437.46
Temperature (K)
120(2)
Wavelength (Å)
0.71073
Crystal system
Space group
Monoclinic
C2/c
a (Å)
b (Å)
c (Å)
 (˚)
28.014 (3)
8.3619 (6)
19.4038 (16)
90
100.170 (2)
90
4473.9 (6)
8
1.299
0.154
 (˚)
 (˚)
V (Å3)
Z
Dcalc (g/cm3)
Absorption coefficient (mm–1)
F (000)
1856
Crystal size (mm)
 Range for data collection (˚)
Index ranges
0.130 × 0.120 × 0.120
3.325-25.247
–33 ≤ h ≤ 32
–10 ≤ k ≤ 10
–23 ≤ l ≤ 23
13183
4032 [Rint = 0.0293]
Multi-scan
1.000 and 0.756
full-matrix least-squares on
F2
Reflections collected
Independent reflections
Absorption correction
Max and min transmission
Refinement method
Data/restraints/parameters
Goodness-of-fit on F2
Final R indices [I> 2σ(I)]
R indices (all data)
4032/0/292
1.061
R1 = 0.0409, wR2 = 0.0991
R1 = 0.0442,wR2 = 0.1021
Largest difference in peak and hole 0.252 and –0.409
(e Å–3)
18
ACCEPTED MANUSCRIPT

ACCEPTED MANUSCRIPT
Table 2 Selected bond lengths (Å) and angles (°).
Theoretical
Experimental
N—
N—
H∙∙∙O═C
1.493
1.735
1.649
1.664
1.233
-
Monomer N—H∙∙∙π
H∙∙∙O═P
1.502
1.710
1.667
1.659
1.236
-
P1-O3
P1-N1
P1-N2
P1-N3
O1-C1
O2-C5
1.489
1.733
1.666
1.665
1.231
-
1.492
1.732
1.668
1.661
1.231
-
1.4792(11)
1.6857(13)
1.6259(14)
1.6225(14)
1.2335(18)
1.370(2)
O2-C8
-
-
-
-
1.428(2)
N1-C1
N2-C9
N3-C17
N1-H1
N2-H2
N3-H3
1.385
1.471
1.463
1.012
1.017
1.013
107.6
113.7
122.3
110.6
99.5
102.0
114.0
118.5
125.1
112.6
114.8
121.3
114.7
115.0
125.0
1.383
1.471
1.462
1.011
1.018
1.016
107.0
113.7
122.3
110.2
100.4
102.2
114.0
118.7
125.3
112.3
114.4
120.9
114.2
114.6
124.5
1.385
1.472
1.461
1.029
1.018
1.012
108.8
111.4
119.8
112.2
101.5
102.9
114.9
121.9
122.4
111.3
114.1
121.1
115.3
115.8
126.1
1.378
1.467
1.463
1.011
1.019
1.012
105.6
112.8
122.2
112.4
100.2
103.1
112.9
118.6
127.9
119.8
115.2
124.4
115.4
115.2
124.4
1.366(2)
1.460(2)
1.454(2)
0.79(2)a
0.82(2)a
0.84(2)a
O3-P1-N1
O3-P1-N2
O3-P1-N3
N1-P1-N2
N1-P1-N3
N2-P1-N3
P1-N1-H1
C1-N1-H1
P1-N1-C1
P1-N2-H2
C9-N2-H2
P1-N2-C9
P1-N3-H3
C17-N3-H3
P1-N3-C17
107.85(6)
109.30(7)
118.97(7)
113.20(7)
102.37(7)
105.17(7)
116.6(14)
119.1(14)
123.73(11)
119.8(13)
113.6(14)
122.51(11)
117.8(13)
116.6(13)
125.39(11)
a These values change to 1.009 Å by using Hirshfeld atom refinement.
19
ACCEPTED MANUSCRIPT

ACCEPTED MANUSCRIPT
Table 3 Hydrogen bond geometry (Å and °).
D—H∙∙∙A
D—H
H∙∙∙A
D∙∙∙A
D—H∙∙∙A
168.9(19)
152.8(18)
162.0(18)
N1—H1∙∙∙O3i 0.79(2)
N2—H2∙∙∙O1ii 0.82(2)
N3—H3∙∙∙Cgiii 0.84(2)
2.00(2)
2.12(2)
2.43(2)
2.7846(17)
2.8756(17)
3.2449(14)
Symmetry codes: (i) ; (ii) ; (iii)
.
20
ACCEPTED MANUSCRIPT

ACCEPTED MANUSCRIPT
Table 4 The AIM results related to the IHB strength of three dimers NCP—H∙∙∙O═P, NP—
H∙∙∙O═C, and
NP—H∙∙∙π calculated at B3LYP/6-311G* level of theory
N—H∙∙∙O═P
N—H∙∙∙O═C
N—H∙∙∙π
ρ(r)
0.031652
0.022054
0.0085424
(ρ(r))
G(r)
0.097992
0.024052
–0.023607
1.01885
0.069864
0.017241
–0.017016
1.013234
0.0259768
0.0054097
–0.004325
1.250798
V(r)
–G(r)/V(r)
EHB
7.41
5.34
1.36
The units of AIM results are: ρBCP (e au–3), 2ρBCP (e au–5), and EHB in kcal/mol
21
ACCEPTED MANUSCRIPT

ACCEPTED MANUSCRIPT
Table5 Selected second order perturbation energies E(2) (donoracceptor)a
N—
H∙∙∙O═P
11.87
N—
H∙∙∙O═C
Donor
O
O
C-
Type
LP (1)
LP (3)
Acceptor
N-H
Type


N—H∙∙∙π
8.25
2.40
-
-
N-H
6.99
C(Ph)
N-H
-
-
1.99


aEnergy in kcal/mol.
22
ACCEPTED MANUSCRIPT

ACCEPTED MANUSCRIPT
Figure 1 Chemical structure of [(4-CH3O)C6H4C(O)NH]P(O)[NHCH2C6H4(4-CH3)]2 (I)
23
ACCEPTED MANUSCRIPT

ACCEPTED MANUSCRIPT
Figure
2
Displacement
ellipsoid
plot
(50
%
probability)
for
[(4-
CH3O)C6H4C(O)NH]P(O)[NHCH2C6H4(4-CH3)]2 with atom numbering scheme. Hydrogen
atoms are drawn as spheres of arbitrary radii.
24
ACCEPTED MANUSCRIPT

ACCEPTED MANUSCRIPT
Figure
3
View of the crystal packing
in the structure of [(4-
CH3O)C6H4C(O)NH]P(O)[NHCH2C6H4(4-CH3)]2, showing N—H∙∙∙O═P, N—H∙∙∙O═C and N—
H∙∙∙π hydrogen bonds as dotted lines. The hydrogen atoms bonded to the carbon atoms were
omitted for clarity (colour key for the atoms: green C, blue N, orange P, red O, and light grey H).
25
ACCEPTED MANUSCRIPT

ACCEPTED MANUSCRIPT
Figure
4
Front and back views of the Hirshfeld surfaces for [(4-
CH3O)C6H4C(O)NH]P(O)[NHCH2C6H4(4-CH3)]2. The interactions according to the labels in the
figures are as follows, with the labels in parentheses: N1-H1∙∙∙O3=P1 (1), N2-H2∙∙∙O1=C1 (2),
C3-H3A∙∙∙O3=P1 (3), C24-H24A∙∙∙O3=P1 (4), N3-H3∙∙∙π (C18 to C22) (5) and C7-H7∙∙∙C10 (6).
26
ACCEPTED MANUSCRIPT

ACCEPTED MANUSCRIPT
a
b
c
d
e
27
ACCEPTED MANUSCRIPT

ACCEPTED MANUSCRIPT
Figure 5 Two-dimensional fingerprint plots of [(4-CH3O)C6H4C(O)NH]P(O)[NHCH2C6H4(4-
CH3)]2: (a) full, (b) H∙∙∙H, (c) C∙∙∙H/H∙∙∙C, (d) O∙∙∙H/H∙∙∙O, (e) N∙∙∙H/H∙∙∙N.
28
ACCEPTED MANUSCRIPT

ACCEPTED MANUSCRIPT
Figure 6 The IR spectrum of [(4-CH3O)C6H4C(O)NH]P(O)[NHCH2C6H4(4-CH3)]2.
29
ACCEPTED MANUSCRIPT