Different orientations of C=O versus P=O in P(O)NHC(O) skeleton: The first study on an aliphatic diazaphosphorinane with a gauche orientation

Article abstract of DOI:10.1007/s11224-010-9682-y

Different orientations of P(O) versus C(O) in P(O)NHC(O) skeleton have been discussed in two new phosphorus(V)-nitrogen compounds with formula XP(O)Y and XP(O)Z₂ where X = NHC(O)C₆H₄ (4-F) and Y = NHCH₂C(CH

Full text of DOI:10.1007/s11224-010-9682-y

Struct Chem (2011) 22:201–210
DOI 10.1007/s11224-010-9682-y
ORIGINAL RESEARCH
Different orientations of C=O versus P=O in P(O)NHC(O)
skeleton: the first study on an aliphatic diazaphosphorinane
with a gauche orientation
•
Atekeh Tarahhomi Mehrdad Pourayoubi
•
•
Arnold L. Rheingold James A. Golen
Received: 14 July 2010 / Accepted: 28 October 2010 / Published online: 25 December 2010
Ó Springer Science+Business Media, LLC 2010
Abstract Different orientations of P(O) versus C(O) in
P(O)NHC(O) skeleton have been discussed in two new
phosphorus(V)-nitrogen compounds with formula XP(O)Y
and XP(O)Z2 where X = NHC(O)C6H4(4-F) and Y =
NHCH2C(CH3)2CH2NH (1), Z = NHC6H4(4-CH3) (2).
Compound 1 is the first example of an aliphatic diaza-
phosphorinane with a gauche orientation which has been
studied by X-ray crystallography; the P=O bond is in the
equatorial position of the ring. Both compounds show
nJ(F,C) and mJ(F,H) coupling constants (n = 1, 2, 3 and 4;
compound 2, containing P=O and C=O bonds in an anti
position, are involving in a stronger N–HꢀꢀꢀO=P hydrogen
bond in crystal network. This leads to a weaker P=O and
N
N
C(O)NHP(O)–H bonds and stronger NꢀꢀꢀO interaction. The
amide–H is involved in an intramolecular N–HꢀꢀꢀO
hydrogen bond.
Keywords Phosphoric triamides ꢀ NMR ꢀ X-ray
crystallography ꢀ Hydrogen bonds ꢀ Chemical calculation
3
m = 3 and 4) and J(P,C) [ 2J(P,C). Quantum chemical
calculations were performed with HF and Density Func-
tional Theory (DFT) methods using 6-31?G(d,p) basis
set. A tentative assignment of the observed vibrational
bands for these molecules is discussed. Compound 1 shows
a deshielded C atom of the carbonyl moiety (in 13C NMR
spectrum) relative to that of 2, which is supported by IR
spectroscopy in which the considerably lower C=O fre-
quency is observed for 1. Comparing the X-ray crystal-
lography and IR spectra of 1 and 2 shows that the acyclic
Introduction
The study on O atoms’ orientation in P(O)NHC(O) moi-
ety of N-carbonyl phosphoramidates is important because
of the structural features, hydrogen bonding patterns, and
binding manner to metal cations [1–5]. The anti orienta-
tion is preferred for the C=O versus P=O unit [6, 7].
Some researchers have employed the anionic form
[P(O)NC(O)]- to obtain compounds with a non-anti ori-
entation [8] and better donority properties [9]. Despite the
numerous structures reported in this series [10–19], there
are a few neutral structures with synclinal orientation
[2, 5, 13–17, 19]. Here, we study on two new compounds
with different orientations of C=O versus P=O. Moreover,
the diazaphosphorinane reported in this work is the first
example of a structurally investigated aliphatic diaza-
phosphorinane with a gauche orientation. The structural
and spectroscopic features of new synthesized compounds
(1 and 2) are studied. Moreover, their optimized geo-
metric parameters and vibrational frequencies are calcu-
lated by theoretical methods (HF and DFT) and a
tentative assignment of the observed vibrational bands is
discussed.
Electronic supplementary material The online version of this
article (doi:10.1007/s11224-010-9682-y) contains supplementary
material, which is available to authorized users.
A. Tarahhomi ꢀ M. Pourayoubi (&)
Department of Chemistry, Ferdowsi University of Mashhad,
Mashhad 91779, Iran
e-mail: mehrdad_pourayoubi@yahoo.com
A. L. Rheingold ꢀ J. A. Golen
Department of Chemistry, University of California, San Diego,
9500 Gilman, Drive, La Jolla, CA 92093, USA
123

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Struct Chem (2011) 22:201–210
Experimental
(2:1 mole ratio) and was stirred at -5 °C for 4 h. After the
solvent was removed, the product was washed with dis-
tilled water and recrystallized from methanol/acetonitrile at
room temperature. IR (KBr, cm-1): m = 3327 (NH), 3199
(NH), 2941, 2230, 1636 (C=O), 1454, 1379, 1281 (P=O),
1209, 1088, 955 (P–Namide), 858, 785 (P–NC(O)NHP(O)),
General methods and materials
1
1H, 13C, H–13C HSQC, 19F, 31P{1H} NMR spectra were
1
recorded on a Bruker Avance DRS 500 spectrometer. H
and 13C chemical shifts were determined relative to TMS,
and 31P and 19F chemical shifts, respectively, relative to
85% H3PO4 and CFCl3 as external standards. Infrared (IR)
spectra were recorded on a Buck 500 scientific spectro-
meter using KBr disc. 4-F-C6H4C(O)NHP(O)Cl2 was
prepared according to the literature method for 4-NO2-
C6H4C(O)NHP(O)Cl2 by using 4-F-C6H4C(O)NH2 instead
of 4-NO2-C6H4C(O)NH2 [7].
668. H NMR (500.13 MHz, DMSO-d6, 300.0 K, TMS):
1
d = 0.76 (s, 3H, CH3), 1.09 (s, 3H, CH3), 2.59 (ddd,
3J(H,H) = 5.3 Hz, 2J(H,H) = 11.7 Hz, 3J(P,H) = 26.3 Hz,
2H, CHequatorial), 3.00 (d, 2J(H,H) = 12.1 Hz, 2H, CHaxial),
3
4.59 (s, 2H, NHamide), 7.28 (t, J[(H,H), (H,F)] = 8.8 Hz,
2H, Ar–H), 8.04 (dd, 3J(H,H) = 8.7 Hz, 4J(H,F) = 5.5 Hz,
2H, Ar–H), 9.30 (s, 1H, NHC(O)NHP(O)). 13C NMR (125.75
MHz, DMSO-d6, 300.0 K, TMS): d = 23.05 (s, 1C, CH3),
24.83 (s, 1C, CH3), 30.22 (d, 3J(P,C) = 4.8 Hz, 1C, CMe2),
53.21 (d, 2J(P,C) = 2.4 Hz, 2C, CH2), 115.16 (d,
2J(F,C) = 21.9 Hz, 2C), 130.35 (dd, 3J(P,C) = 7.6 Hz,
4J(F,C) = 2.7 Hz, 1C, Cipso), 130.81 (d, 3J(F,C) = 9.2 Hz,
X-ray measurements
A colorless crystal of compound 1 was mounted on a
Mitegen Micromount with Bruker uv adhesive and was then
automatically centered on a Bruker SMART X2S benchtop
crystallographic instrument. Intensity measurements were
performed using a monochromated (Doubly Curved Silicon
1
2C), 164.29 (d, J(F,C) = 249.5 Hz, 1C), 167.67 (s, 1C,
C=O). 31P{1H} NMR (202.45 MHz, DMSO-d6, 300.0 K,
H3PO4 external): d = 2.15 (s). 19F NMR (470.59 MHz,
DMSO-d6, 300.0 K, CFCl3): d = -108.77 (m).
˚
Crystal) Mo Ka radiation (0.71073 A) from a sealed Micro
Focus tube. Data were acquired under a stream of dry cold air
at 200(2) K using three sets of omega scans at different phi
settings with frame width of 0.5° and an exposure time of
30 s/frame. Apex 2 software was used for preliminary
determination of the unit cell and determination of integral
intensities and unit cell refinement were performed using
SAINT. Data was corrected for absorption using SADABS
and structure was solved by direct methods. A colorless
crystal of sample 2 was mounted on a Cryoloop with Par-
atone-N oil. Data were collected on a Bruker APEX CCD
X-ray system using Mo Ka radiation in a nitrogen gas stream
at 100(2) K using phi and omega scans with frame width of
0.5° and exposure time of 10 s/frame. Data was integrated
using the Bruker suite of software programs [20], corrected
for absorption using SADABS and structure was solved by
direct methods. For both structures all non-hydrogen atoms
were refined anisotropically by full-matrix least-squares on
F2 (SHELXL-97) [21] and hydrogen atoms on atoms N1, N2,
and N3 were found from a Fourier difference map and were
allowed to refine. All other hydrogen atoms were placed in
calculated positions with appropriate riding models.
N-(4-Fluorobenzoyl)-N0,N00-bis (4-methyl-phenyl)
phosphoric triamide (2)
To a solution of 4-F-C6H4C(O)NHP(O)Cl2 in chloroform, a
solution of p-toluidine and triethylamine (1:2:2 mole ratio)
in chloroform were added at -5 °C. After 4 h stirring, the
solvent was removed and product was washed with dis-
tilled water and recrystallized from methanol/n-heptane at
room temperature. IR (KBr, cm-1): m = 3270 (NH), 3091
(NH), 2920, 1656 (C=O), 1520, 1446, 1379, 1228 (P=O),
1
1101, 945, 824 (P–Namide), 746 (P–NC(O)NHP(O)). H NMR
(500.13 MHz, DMSO-d6, 300.0 K, TMS): d = 2.16 (s, 6H,
3
2CH3), 6.96 (d, J(H,H) = 7.7 Hz, 4H, Ar–H), 7.05 (d,
3J(H,H) = 8.1 Hz, 4H, Ar–H), 7.28 (t, 2H, Ar–H), 7.69 (d,
2J(P,H) = 9.4 Hz, 2H, NH), 7.99 (m, 2H, Ar–H), 9.88 (s,
1H, NHC(O)NHP(O)). 13C NMR (125.75 MHz, DMSO-d6,
300.0 K, TMS): d = 20.17 (s, 2C, CH3), 115.29 (d,
2J(F,C) = 21.9 Hz, 2C), 117.84 (d, 3J(P,C) = 7.2 Hz, 4C),
129.15 (s, 4C), 129.20 (s, 2C), 129.85 (dd, 1C, Cipso),
3
130.95 (d, J(F,C) = 9.3 Hz, 2C), 138.61 (s, 2C), 164.48
(d, 1J(F,C) = 250.1 Hz, 1C), 166.85 (s, 1C, C=O). 31P{1H}
NMR (202.45 MHz, DMSO-d6, 300.0 K, H3PO4 external):
d = -4.61 (s).
Syntheses
Computational approaches
5,5-Dimethyl-2-[N-(4-fluorobenzoyl)]-2-oxo-1,3,
2-diazaphosphorinane (1)
All calculations [Density functional (DF) and Hartree–
Fock (HF)] were performed using the Gaussian 03W
program package [22] and Gauss-View 3.07 molecular
visualization program [23] and the X-ray data (cif files)
2,2-Dimethyl-1,3-propanediamine was added dropwise
to a solution of 4-F-C6H4C(O)NHP(O)Cl2 in chloroform
123

Struct Chem (2011) 22:201–210
203
were used as the initial structure. Among the variety of
functionals, including nonlocal corrections, we used
Becke’s three-parameter hybrid functional using the Lee–
Yang–Parr correlation functional (B3LYP) [24]. Geometry
optimization and calculation of vibrational frequencies
were investigated with the widely used 6-31?G(d,p) basis
set for both HF and DFT methods. No scale factor was used
in the calculated frequencies.
angles of about 70° for P–N–C–Haxial and 170° for
P–N–C–Hequatorial obtained from X-ray crystallography, the
3
value of 26.3 Hz is assigned to J(PNCHequatorial). This is
larger than the 3J(PNCH) values for acyclic phosphor-
amidates, for example in compound CCl3C(O)NHP(O)
[N(CH3)(CH2C6H5)]2 3J(P,H) = 10.2 and 9.1 Hz for CH3
and CH2 units [10]. The phosphorus–Haxial coupling is not
observed. Two doublet signals at 30.22 and 53.21 ppm in
13C NMR spectrum of 1 are, respectively, assigned to the
carbon atoms with three- and two-bond separations from
3
Results and discussion
phosphorus with J(P,C) = 4.8 [ 2J(P,C) = 2.4 Hz. This
is in agreement with the previously reported diazaphos-
phorinane compounds [26] and compounds with cyclic
five- and six-membered ring amide groups linked to P
atom, and in contrast with the reported acyclic amides such
as N(CH2CH3)2 and N(CH2CH3)(CH2C6H5) which show
2J(P,C) [ 3J(P,C) [27] (NR1R2 is introduced as an amide
moiety, where R1 and/or R2 are H, alkyl, or aryl). More-
over, in the 4-F-C6H4C(O)NHP(O) moiety, 3J(P,C) =
7.6 [ 2J(P,C) = 0.0 Hz. A similar observation is found
Heterocyclic compound 1 (Scheme 1, right) was synthe-
sized by the reaction of 4-F-C6H4C(O)NHP(O)Cl2 and two
times mole ratio of diamine (one half as nucleophile and
others as HCl scavenger). Compound 2 (Scheme 1, left)
was prepared in a similar manner but by using triethyl-
amine as an organic base instead of the excess amount of
amine. The phosphoramide functional group is NHP(O).
Two different types of this functional group, NHP(O) and
C(O)NHP(O) in compounds 1 and 2, are introduced as
Namide and NC(O)NHP(O) for their related nitrogen atoms in
the next sections of paper.
3
for compound 2: J(P,C) [ 2J(P,C) in both 4-F-C6H4C(O)
NHP(O) and P(O)[NHC6H4-(4-CH3)] moieties. In contrast
to NHCH2C(CH3)2CH2NH in compound 1, the NH proton
of the 4-CH3-C6H4NH moiety in 2 reveals as a doublet
signal (2J(P,H) = 9.4 Hz). Compounds 1 and 2 show
mJ(F,H) and nJ(F,C) coupling constants (m = 3 and 4;
n = 1, 2, 3, and 4). For example, in compound 1:
3J(H,F) = 8.8 Hz, 4J(H,F) = 5.5 Hz (these fluorine-
hydrogen couplings lead to the multiplet peak in 19F NMR
NMR studies
The related signals of Haxial and Hequatorial in compound 1
can be differentiated by their different splitting patterns.
Considering the Karplus equation [25] and the torsion
1
spectrum, Fig. S1 in Supplementary material), J(F,C) =
249.5 Hz, 2J(F,C) = 21.9 Hz, 3J(F,C) = 9.2 Hz,
F
1
4J(F,C) = 2.7 Hz. To confirm this assignment, the H–13C
HSQC (H–C correlation spectrum) spectrum was obtained
for compound 1 (Fig. S2 in Supplementary material) which
shows the signals at 7.28 and 8.04 ppm (showing the
3J(H,F) and 4J(H,F)) in 1H NMR spectrum are related,
respectively, to the carbon atoms at 115.16 and 130.81 ppm
(showing 2J(F,C) and 3J(F,C)) in 13C NMR spectrum.
Compound 1 with a gauche orientation of C=O versus P=O
shows a deshielded carbon atom of carbonyl moiety rela-
tive to that of 2 (167.67 ppm for 1 and 166.85 ppm for 2).
This is supported by IR spectroscopy in which a lower
C=O frequency is observed for 1 (1636 vs 1656 cm-1
for 2).
F
1.369(2)
O
NH
1.352(3)
1.676(2)
HN
O
P
H
HN
HN
O
1.700(2)
P
N
O
H3C
H
N
Structural description
CH3
Single crystals of compounds 1 and 2 were, respectively,
obtained from CH3OH/CH3CN and CH3OH/n-C7H16 at r.t.
Crystallographic data and the details of X-ray analysis are
presented in Table 1; selected experimental (X-ray) and
calculated (at 6-31?G(d,p) basis set) geometrical
parameters are given in Table 2. The molecular structures
H3C
CH3
Scheme 1 The non-anti orientation of P(O) versus C=O (right,
compound 1) and anti orientation (left, compound 2), the values in the
˚
scheme are the bond lengths (A)
123

204
Struct Chem (2011) 22:201–210
Table 1 Crystal data and structure refinement for compounds 1 and 2
Compound 1
Compound 2
Empirical formula
Formula weight
Temperature (K)
C12H17FN3O2P
285.26
C21H21FN3O2P
397.38
200(2)
100(2)
˚
Wavelength (A)
0.71073
0.71073
Monoclinic
C2/c
Crystal system
Space group
Orthorhombic
Pca2(1)
˚
a = 10.269(3) A
˚
a = 24.712(6) A
Unit cell dimensions
˚
b = 13.204(3) A
˚
b = 17.238(4) A
˚
c = 10.238(2) A
˚
c = 9.874(3) A
b = 110.052(4)°
3951.1(17)
3
˚
Volume (A )
1388.1(6)
Z
4
8
Density (calculated) (Mg/m3)
Absorption coefficient (mm-1
F(000)
1.365
1.336
)
0.211
0.170
600
1664
Crystal size (mm3)
0.50 9 0.15 9 0.15
Colorless/block
2.51–28.11
0.45 9 0.10 9 0.10
Colorless/block
1.47–27.91
Crystal color/habit
Theta range for data collection (°)
Index ranges
-12 B h B 13
-17 B k B 17
-13 B l B 13
10,526
-32 B h B 32
-22 B k B 22
-12 B l B 12
16,310
Reflections collected
Independent reflections
Completeness to theta = 25.00°
Absorption correction
3,169 [R(int) = 0.0528]
99.90%
4,456 [R(int) = 0.0508]
96.90%
Multi-scan/sadabs
0.9690 and 0.9016
Full-matrix least-squares on F2
3169/1/186
Multi-scan/sadabs
0.9832 and 0.9274
Full-matrix least-squares on F2
4456/0/267
Max. and min. transmission
Refinement method
Data/restraints/parameters
Goodness-of-fit on F2
1.011
1.036
Final R indices [I [ 2sigma(I)]
R indices (all data)
R1 = 0.0460, wR2 = 0.0915
R1 = 0.0648, wR2 = 0.0980
-0.06(11)
R1 = 0.0467, wR2 = 0.1091
R1 = 0.0757, wR2 = 0.1235
–
Absolute structure parameter
-3
˚
Largest diff. peak and hole (eꢀA
)
0.316 and -0.228
0.274 and -0.393
of 1 and 2 are shown in Figs. 1 and 2, respectively. The
phosphorus atoms have a distorted tetrahedral configura-
tion with the bond angles in the range of 101.29(12)°
[N(2)–P(1)–N(3)] to 114.74(11)° [O(1)–P(1)–N(1)] for 1
and 103.86(8)° [N(3)–P(1)–N(1)] to 115.99(9)° [O(1)–
P(1)–N(3)] for 2. The phosphoryl and carbonyl groups
adopt an anti position in 2, whereas they are in a gauche
situation in 1. Many phosphoric triamides of the type
RC(O)NHP(O)[NR1R2]2 have been investigated structur-
ally [1, 2, 5–7, 10, 11, 13–19, 27–55]; however, the non-
anti orientation has been observed for a few molecules [2,
5, 13–19]. In Tables S1 and S2 (Supplementary material),
some structural parameters of selected molecules with
different conformations are gathered. The O=P–N–C
dihedral angles vary in the range of nearly 180° to 150°
and -62.3(3)° to -53.07(8)° for molecules with anti and
gauche conformations, Table S2 in Supplementary mate-
rial. Moreover, the P–NC(O)NHP(O)–C bond angles show a
slight differences, Table S1 in Supplementary material; so
that the P–NC(O)NHP(O)–C angle (h in Table S1, Supple-
mentary material) has a lower value in most cases of a
gauche orientation, for example h = 120.5(2)° (for 1) and
123.40(13)° (for 2). Considering the present work, up to
now, the structures of two diazaphosphorinanes with a
C(O)NHP(O) skeleton have been studied (entries 2 and
23); so that the diazaphosphorinane 1 (entry 23) is
the first example of a structurally investigated aliphatic
diazaphosphorinane with
a gauche orientation. The
123

Struct Chem (2011) 22:201–210
205
˚
Table 2 Selected bond distances (A) and angles (°) for compounds 1 and 2
Parameter
Compound 1
Compound 2
HF/6-31?G(d,p) B3LYP/6-31?G(d,p) X-ray
X-ray
HF/6-31?G(d,p) B3LYP/6-31?G(d,p)
Length bonds
P=O
1.4725(19) 1.456
1.485
1.741
1.672
1.680
1.230
1.477
1.476
1.380
1.356
1.4755(13) 1.458
1.6756(17) 1.700
1.6450(17) 1.653
1.6296(16) 1.656
1.486
1.729
1.672
1.680
1.235
1.421
1.423
1.376
1.355
P–NC(O)NHP(O)
P–N(1)amide
P–N(2)amide
C=O
1.700(2)
1.631(2)
1.629(2)
1.232(3)
1.474(3)
1.468(3)
1.352(3)
1.358(3)
1.712
1.648
1.657
1.202
1.463
1.464
1.368
1.329
1.233(2)
1.427(2)
1.412(2)
1.369(2)
1.357(2)
1.207
1.419
1.420
1.363
1.328
C–N(1)amide
C–N(2)amide
C–NC(O)NHP(O)
C–F
Angles
O=P–N(1)amide
O=P–N(2)amide
O=P–NC(O)NHP(O)
114.74(11) 115.59
113.91(12) 114.81
110.34(11) 113.67
105.32(12) 104.25
110.32(11) 107.47
101.29(12) 99.42
119.72(18) 119.88
120.29(19) 119.72
116.05
114.87
113.61
104.57
106.87
99.11
115.99(9)
114.01(8)
107.85(8)
104.60(8)
103.86(8)
110.01(8)
117.54
114.42
107.61
105.01
103.21
108.21
118.80
114.53
107.83
104.43
102.17
108.02
125.93
126.46
125.88
120.64
N
N
N
amide–P–Namide
(1)amide–P–NC(O)NHP(O)
(2)amide–P–NC(O)NHP(O)
P–N(1)amide–C
119.17
119.38
124.56
121.71
124.69(14) 125.10
128.70(13) 125.10
123.40(13) 125.99
120.31(18) 120.78
P–N(2)amide–C
P–NC(O)NHP(O)–C
N–C=O
120.5(2)
120.9(2)
124.57
121.70
Torsion angles
O=P–NC(O)NHP(O)–C
P–NC(O)NHP(O)–C=O
-57.2(2)
-12.6(3)
-75.65
-16.79
53.57
-79.67
-15.13
49.64
176.85(14) 178.36
-178.77
9.10
8.7(2)
-59.54(16) -56.69
51.94(17) 54.24
8.74
C–NC(O)NHP(O)–P–N(1)amide 70.6(2)
-52.81
56.96
C–NC(O)NHP(O)–P–N(2)amide -178.2(2) 161.86
157.99
Fig. 1 Molecular structure and
atom labeling scheme for
compound 1 with displacement
ellipsoids at the 50% probability
level
˚
C–NC(O)NHP(O) bond length in 1 is shorter than that of 2 and
the opposite is observed for the P–NC(O)NHP(O) bond length,
˚
Scheme 1. The P=O bond lengths of 1.4725(19) A (1) and
˚
1.4755(13) A (2) are standard for the phosphoric triamide
˚
compounds. The P–NC(O)NHP(O) in 1 (1.700(2) A) is
˚
slightly longer than that of 2 (1.6756(17) A). The P–Namide
˚
bond lengths of 1.629(2) and 1.631(2) A in 1 and
1.6296(16) and 1.6450(17) A in 2 are significantly shorter
than the related P–NC(O)NHP(O). In both structures, the N
atoms are almost planar and they do not form any HB as an
acceptor, thus exhibiting low Lewis-base character. Devi-
ation from planarity in nitrogen atoms of the diazaphos-
phorinane moiety in 1 is more than that of P(O)[NHC6
H4(4-CH3)]2 moiety in 2. As expected, the C–NC(O)NHP(O)
123

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Struct Chem (2011) 22:201–210
F
O
HN
P
N
H3C
O
N
CH3
Scheme 2 The endo anomeric effect in 1,3,2-diazaphosphorinane 1;
for related literature about endo anomeric effect in 1,3,2-oxazaphos-
phorinanes, see Ref. [56]
Fig. 2 Molecular structure and atom labeling scheme for compound
2 with displacement ellipsoids at the 50% probability level
˚
Table 3 Hydrogen bonds for compounds 1 and 2 (A and °)
D–HꢀꢀꢀA
d(D–H) d(HꢀꢀꢀA) d(DꢀꢀꢀA) \(DHA)
˚
bond lengths of 1.352(3) A (1) and 1.369(2) A (2) were
˚
Compound 1
N(3)–H(3C)ꢀꢀꢀO(1)#1 0.82(3)
N(2)–H(2A)ꢀꢀꢀO(2)#2 0.79(3)
N(1)–H(1C)ꢀꢀꢀO(1)#3 0.81(3)
2.08(3)
2.25(3)
2.54(3)
2.77(3)
2.885(3) 168(2)
3.019(3) 166(3)
3.183(3) 138(3)
3.184(3) 113(3)
found to be shorter than the other C–N bond lengths
˚
˚
(1.474(3) and 1.468(3) A in 1 and 1.412(2) and 1.427(2) A
in 2). In diazaphosphorinane ring, the P=O bond is placed
in an equatorial position, attributed to the endo anomeric
effect which was previously observed by Bentrude for
1,3,2-oxazaphosphorinane [56]. Moreover, this configura-
tion has been found for another derivative of diazaphos-
phorinane family reported by Gholivand et al. [57]. This
situation is observed for 1 probably via overlapping of the
non-bonding orbital located on the endocyclic nitrogen
atoms with the anti-bonding orbital of P–N(exocyclic)
[56]. This n to r* overlap should stabilize the lying of
PꢁNNHCðOÞC H ꢁF bond in axial position (Scheme 2). This
N(1)–H(1C)ꢀꢀꢀO(2)
0.81(3)
Compound 2
N(1)–H(1B)ꢀꢀꢀO(1)#1 0.79(2)
N(2)–H(2B)ꢀꢀꢀO(2)#2 0.83(2)
2.00(2)
2.08(3)
2.39(2)
2.792(2) 173(2)
2.897(2) 170(2)
2.959(2) 128(2)
N(3)–H(3B)ꢀꢀꢀO(2)
0.82(2)
Symmetry transformations used to generate equivalent atoms for
compound1:#1 –x ? 1/2, y, z ? ‘;#2 x ? 1/2, -y ? 1,z;#3 x - 1/2,
-y ? 1, z; for compound 2: #1 –x ? 1, y, -z ? ‘; #2 –x ? 1, y,
-z ? 3/2
4
6
overlap helps to decrease the pyramidality of the N atoms.
The crystal packing adopted allows putting the benzoyl
substituent in a position where it has the less steric effect.
The HB interactions lead to a 2-D network parallel to
the [010] plane. This arrangement is composed of cyclic
tetramer motifs via two different types intermolecular
N–HꢀꢀꢀO hydrogen bonds (N(3)–H(3C)ꢀꢀꢀO(1) and N(2)–
H(2A)ꢀꢀꢀO(2) HBs, Table 3). This motif is a result of the
gauche orientation of P=O versus C=O, due to the suitable
arrangement of oxygen atoms which are gathered mole-
cules in a cyclic arrangement through HBs, see the pink-
colored molecule in Fig. 3. Each molecule contains two
H-acceptor centers (O atoms) which involve them with two
H-donor sites (N atoms) in the normal HB interactions; i.e.,
one of the Namide–H units does not cooperate in the normal
HB interaction (it cooperates in a weak HB). So, the four
interacting molecules (within the tetramer motif) provide
the following interacting sites: (a) two H-acceptor sites by
the first molecule, (b) two H-donor sites by the second one,
c and d) both two other molecules provide one H-acceptor
and one H-donor in which one of them provides the C=O
and the nitrogen atom of C(O)NHP(O) moiety and the
other its P=O and the Namide–H unit, Fig. 3. The other
possible interacting sites, which are not involved within the
mentioned tetramer, are responsible for the interaction of
the tetramer with the neighboring tetramers. This causes to
123

Struct Chem (2011) 22:201–210
207
of compound 1 [N(3)–H(3C)ꢀꢀꢀO(1) and N(2)–H(2A)ꢀꢀꢀO(2)
HBs], compound 2 is also exhibited along with hydrogen
bonding interactions involving the oxygen atoms (of P=O
and C=O) and the H-donor sites, H–NC(O)NHP(O) and
H–Namide. The anti orientation is responsible to form the
extended chain in the crystal network which is parallel to
the c axis. Furthermore, both P=OꢀꢀꢀH–NC(O)NHP(O) and
C=OꢀꢀꢀH–Namide hydrogen bonds are slightly stronger than
the similar HBs in compound 1. These observations are
supported by IR spectra in which the lower N–H and P=O
frequencies are found for 2 that those of observed for 1.
Moreover, an intramolecular HB exists between the
N
amide–H and the carbonyl’ O atom which is responsible to
lowering Namide–H frequency in 2 which will discuss later.
A fragment of crystal packing viewed along the c axis is
shown in Fig. 5.
Theoretical studies
Fig. 3 Cyclic tetramer motif in crystal structure of 1, the H-acceptor
atoms in the tetramer are shown with red balls and the H-donor with
blue balls; the gauche orientation of P=O versus C=O allows to
arrange the molecule in a cyclic motif (Color figure online)
Geometry optimization
The geometries of compounds 1 and 2 were optimized using
the HF and DFT methods (the B3LYP functional) with
6-31?G(d,p) basis set. The optimized geometric parame-
ters are shown in Table 2. By comparison, all bond lengths
obtained by the DFT method are longer than those of HF,
and, overall, better bond length prediction is achieved with
DFT. For instance, C=O and C–F bond lengths in 1 and 2
are better predicted by DFT with a difference from exper-
lay one tetramer between eight other tetramers. Moreover,
if the weaker intramolecular N(1)–H(1C)ꢀꢀꢀO(2) and
intermolecular N(1)–H(1C)ꢀꢀꢀO(1) hydrogen bonds have
also been considered, the arrangement is still a 2-D array;
i.e., these HBs have little influence on the architecture of
the molecules in the network but they help in the stabil-
ization of crystal packing. A fragment of crystal packing
viewed along the a axis is shown in Fig. 4. Similar to HBs
˚
imental values about 0.002 A for both. The HF method is
slightly better than the DFT method for the bond angles
Fig. 4 A fragment of crystal
packing of 1
123

208
Struct Chem (2011) 22:201–210
Table 4 Selected calculated and experimental vibrational data
(cm-1) for compounds 1 and 2 using HF and DFT methods with
6-31?G(d,p) basis set
Experimental
Calculated
Tentative assignment
HF
DFT
Compound 1
3199(s)
3883
3824
3158
1922
1597
3617
3594
2988
1725
1430
t (NC(O)NHP(O)–H)
t (Namide–H)
ts CH2
3327(s)
2941(s)
1636(vs)
1454(s)
t (C=O)
t (OC–NC(O)NHP(O)) ?
d (NC(O)NHP(O)–H)
1281(m)
1088(s)
955(m)
1374
1175
1038
928
1260
1078
956
t (P=O)
tas (C–Namide) ? q CH3
tas (P–Namide) ? q CH3 ? s CH2
c (C–H) ring
858(s)
868
785(m)
895
796
t (P–NC(O)NHP(O)) ? D ring
c (NC(O)NHP(O)–H) ? D ring
668(m)
692
644
Compound 2
3091(s)
3270(s)
2920(s)
1656(vs)
1520(s)
1446(s)
3875
3818
3180
1897
1608
1552
3619
3525
3030
1706
1507
1458
t (NC(O)NHP(O)–H)
t (Namide–H)
ts CH3
t (C=O)
d CH3
t (OC–NC(O)NHP(O)) ?
d (NC(O)NHP(O)–H)
1228(vs)
1101(w)
946(s)
1347
1114
1013
925
1273
1034
933
t (P=O)
D ring ? d (C–H) ring
tas (P–Namide) ? c (C–H) ring
c (C–H) ring
824(s)
826
746(s)
872
793
t (P–NC(O)NHP(O))
t Stretching, d in plane bending, c out of plane bending, s twisting,
q rocking, D in plane ring deformation
Fig. 5 A fragment of crystal packing of 2
(Table 2). In general, the optimized geometries of 1 and 2
are in good agreement with the experimental ones, and the
general trends observed in the experimental data are well
reproduced in the calculations.
about the 1200 cm-1 wave number (for example, in 1, at
1281 cm-1) is assigned to the stretching vibration of
the phosphoryl group. The NC(O)NHP(O)–P and Namide–P
stretching modes, the other characteristic fundamentals for
this class of phosphoric triamide compounds, are observed
in the 900–700 cm-1 region. These fundamental modes
appear at 746 cm-1 (calculated: 793 cm-1) and 946 cm-1
(calculated: 933 cm-1) in IR spectrum of 2, respectively.
Moreover, two vibrational modes at 1088 and 668 cm-1 in 1
are, respectively, attributed to the C–Namide stretching and
the NC(O)NHP(O)–H out of plane bending modes. Also, in 2,
the vibrational mode at 1101 cm-1 is assigned to the in plane
ring deformation coupled with the bending mode of C–H
(aromatic). The experimental t(NC(O)NHP(O)–H) frequency
appears at lower frequency relative to the calculated one and
then relative to experimental t(Namide–H) frequency. This is
attributed to the presence of relatively strong HB between
Vibrational frequencies
The vibrational frequencies are computed for the optimized
structures of molecules 1 and 2, by the DFT (B3LYP) and
HF methods using the 6-31?G(d,p) basis set. The most
important experimental and calculated absorption bands are
listed in Table 4. The observed bands are assigned by
comparison of the calculated frequencies with experimental
IR spectra of related molecules [58, 59]. The N–H bending
modes occur in the 1600–1450 cm-1 region. For example,
the experimental value of 1446 cm-1 for d(NC(O)NHP(O)–H)
in 2 is supported by calculation (Table 4). The frequency
123

Struct Chem (2011) 22:201–210
209
the NC(O)NHP(O)–H acidic proton and the phosphoryl group
of neighboring molecule in solid state. It had been found that
[5] the coordination to the metal cation breaks this type
of P=OꢀꢀꢀH–N intermolecular HB leading to the higher
m(NC(O)NHP(O)–H) frequencies for complexes in the
3325–3345 cm-1 range. Considering the experimental and
calculated values of these stretching modes in the molecules
only containing Namide and individually the molecules only
having NC(O)NHP(O), with formula R1P(O)[NHR]2 [58] and
RC(O)NHP(O)Cl2 [59], confirm this assignment. In mole-
cule C6H5OP(O)(NHC6H11)2, the experimental frequency
data can be obtained free of charge from The Cambridge
Crystallographic Data Centre via www.ccdc.cam.ac.uk/
data_request/cif.
Acknowledgments Support of this investigation by Ferdowsi
University of Mashhad is gratefully acknowledged. The authors wish
to thank Bruker AXS, Inc. (Madison, WI) for the use of one of their
SMART X2S benchtop instruments.
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