Synthesis, spectroscopic study, X-ray crystallography and ab initio calculations of the two new phosphoramidates: C6H5OP(O)(NHC6H11)2 and [N(CH3)(C6H11)]P(O)(2-C5

Article abstract of DOI:10.1016/j.molstruc.2007.03.047

Two new phosphoramidates with formula C₆H₅OP(O)(NHC₆H₁₁)₂ (1) and [N(CH₃)(C₆H₁₁)]P(O)(2-C₅H₄N-NH)₂ (2) were synthesized and characteri

Full text of DOI:10.1016/j.molstruc.2007.03.047

Journal of Molecular Structure 874 (2008) 178–186
www.elsevier.com/locate/molstruc
Synthesis, spectroscopic study, X-ray crystallography
and ab initio calculations of the two new phosphoramidates:
C6H5OP(O)(NHC6H11)2 and [N(CH3)(C6H11)]P(O)(2-C5H4N-NH)2
a,
b,c,
b
*
Khodayar Gholivand , Carlos O. Della Vedova *, Mauricio F. Erben ,
´
a
a
a
Hamid Reza Mahzouni , Zahra Shariatinia , Shadi Amiri
a
Department of Chemistry, Tarbiat Modarres University, P.O. Box 14115-175, Tehran, Iran
CEQUINOR (UNLP-CONICET), Departamento de Quı´mica, Facultad de Ciencias Exactas, Universidad Nacional de La Plata,
C.C. 962 (B1900AJL), La Plata, Buenos Aires, Argentina
b
c
Laboratorio de Servicios a la Industria y al Sistema Cientı´fico (UNLP-CIC-CONICET) Gonnet, Buenos Aires, Argentina
Received 4 December 2006; received in revised form 26 March 2007; accepted 26 March 2007
Available online 3 April 2007
Abstract
Two new phosphoramidates with formula C6H5OP(O)(NHC6H11)2 (1) and [N(CH3)(C6H11)]P(O)(2-C5H4N-NH)2 (2) were synthe-
sized and characterized by 1H, 13C, 31P NMR and IR spectroscopies and elemental analyses. The crystal structures of these compounds
˚
˚
˚
ꢀ
were determined using X-ray crystallography. Compound 1 [triclinic, P1, a = 8.8679(16) A, b = 10.230(2) A, c = 12.511(2) A,
a = 95.918(4)ꢀ, b = 103.948(4)ꢀ, c = 110.818(4)ꢀ, Z = 2] forms a centrosymmetric dimmer via two equal intermolecular P@Oꢀ ꢀ ꢀHAN
hydrogen bonds. In this structure, intermolecular hydrogen bonds are also formed between the crystallization solvent and phosphoram-
˚
˚
˚
idate molecules. Compound 2 [monoclinic, P21/c, a = 11.4760(7) A, b = 18.5607(12) A, c = 8.6227(6) A, b = 108.751(5)ꢀ, Z = 4] pro-
duces a one-dimensional polymeric chain through intermolecular P@Oꢀ ꢀ ꢀHAN hydrogen bonds, and a weaker intramolecular
Nꢀ ꢀ ꢀHAN hydrogen bond has been also observed in the crystal. Ab initio quantum chemical calculations were performed for molecules
1 and 2 by the density functional three-parameter hybrid (DFT/B3LYP) and the Hartree–Fock (HF) methods, using the 6-31G* basis set.
The compound 1:CH3OH pair was also calculated as observed in the crystal. The computed geometrical parameters are in good agree-
ment with the experimental results.
ꢁ 2007 Elsevier B.V. All rights reserved.
Keywords: Phosphoramide compounds; NMR spectroscopy; X-ray crystallography; Ab initio quantum chemical calculations
1. Introduction
considered the substituent effects on the NMR and IR
spectra of phosphoramidicacid esters [6,7], and various the-
ories about the steric and electronic effects on phosphorus
chemical shifts in phosphoryl compounds have been
reviewed [8]. The synthesis, structures and complexation
of some phosphoramides have been also reported [9,10].
Furthermore, ab initio studies were performed on different
molecular derivatives of phosphine oxide and sulfide
[11,12], polyphosphorus acid anhydrides [13], phosphates
[14], phosphinates [15] and phosphonates [16–19]. The first
evidence for a catalytic bridging in the active site of
phosphodiesterase was obtained by computational meth-
ods [20]. Herein, we have investigated the synthesis,
Compounds with phosphorus-containing structures are
an important part of chemistry, because of their applica-
tions in medicine [1,2], fertilizers, pesticides and plant
growth regulators [3]. Recently, research on phosphora-
mides attracted attention due to their different applications
in agriculture [4] and biochemistry [5]. Many authors have
*
Corresponding authors. Tel.: +98 021 88011001x4422; fax: +98 021
88009730.
E-mail addresses: gholi_kh@modares.ac.ir (K. Gholivand), carlosdv@
quimica.unlp.edu.ar (C.O. Della Vedova).
´
0022-2860/$ - see front matter ꢁ 2007 Elsevier B.V. All rights reserved.
doi:10.1016/j.molstruc.2007.03.047

K. Gholivand et al. / Journal of Molecular Structure 874 (2008) 178–186
179
spectroscopic characterization, X-ray crystal structures and
ab initio quantum chemical calculations of two new phos-
phoramides with formula C6H5OP(O)(NHC6H11)2 (1)
and [N(CH3)(C6H11)]P(O)(2-C5H4N-NH)2 (2). The experi-
mental data were supplemented by using ab initio (HF) and
DFT (B3LYP) quantum chemical calculations.
78%. m.p. 118 ꢀC. Anal. Calc. for C18H29N2O2P: C
64.26, H 8.68, N 8.33. Found: C 64.24, H 8.67, N 8.32%.
31P NMR (d6-DMSO): 10.81 (m). 13C NMR (d6-DMSO):
24.96 (s), 25.16 (s), 35.11 (d, 3J(P,C) = 5.0 Hz, CH2),
35.22 (d, 3J(P,C) = 5.0 Hz, CH2), 50.01 (s), 120.30 (d,
3J(P,C) = 4.9 Hz, Cortho), 123.18 (s), 129.10 (s), 151.93 (d,
1
2J(P,C) = 6.4 Hz, Cipso). H NMR (d6-DMSO): 1.00–1.17
2. Experimental
(m, 10H), 1.47–1.75 (m, 12H), 2.86 (m, 2H), 4.49 (dd,
2J(P,H) = 10.2 Hz, 3J(H,H) = 9.5 Hz, 2H, NH), 7.05 (t,
3
2.1. Spectroscopic measurements
1H, 13C and 31P NMR spectra were recorded on a Bru-
3J(H,H) = 7.6 Hz, 1H, Ar-H), 7.15 (d, J(H,H) = 7.6 Hz,
2H, Ar-H), 7.28 (t, 3J(H,H) = 7.6 Hz, 2H, Ar-H). IR
(KBr, cmꢁ1): 3230 (m), 2920 (s), 1585 (m), 1484 (s), 1439
(s), 1222 (m), 1199 (s, mP@O), 1166 (w), 1099 (s), 1021
(m), 938 (m), 910 (s), 747 (s), 610 (w), 580 (m).
ker Avance DRS 500 spectrometer. H and 13C chemical
1
shifts were determined relative to internal TMS, 31P chem-
ical shifts relative to 85% H3PO4 as external standard.
Infrared (IR) spectra of solid compounds in KBr pellets
were recorded on a Shimadzu model IR-60 spectrometer.
Elemental analyses were performed using a Heraeus
CHN-O-RAPID apparatus. Melting points were obtained
with an Electrothermal instrument. C6H5OP(O)Cl2 [21]
and [N(CH3)(C6H11)]P(O)Cl2 [22] were synthesized accord-
ing to the literature method.
2.4.2. N-methylcyclohexyl-N0,N00-bis(2-pyridinyl)
phosphoric triamide (2)
To a stirred solution of N-methylcyclohexyl phosphora-
mide dichloride (2.31 g, 10 mmol) in dry acetonitrile
(30 ml), a solution of 2-aminopyridine (3.76 g, 40 mmol)
was added dropwise at ꢁ5 ꢀC. After 15 h, the solvent was
evaporated under vacuum and the oily product was washed
with distilled water and recrystallized from a mixture of
CH3OH/H2O. Yield: 73%. m.p. 225 ꢀC. Anal. Calc. for
C17H24N5OP: C, 59.12; H, 7.00; N, 20.28. Found: C,
59.10; H, 7.01; N, 20.27%. 31P NMR (d6-DMSO): 3.66
(m). 13C NMR (d6-DMSO): 25.03 (s), 25.57 (s), 27.52 (d,
2J(P,C) = 5.4 Hz, N-CH3), 30.02 (d, 3J(P,C) = 2.4 Hz,
CH2), 54.11 (s), 111.18 (d, 3J(P,C) = 4.1 Hz, Cortho),
116.13 (s), 137.62 (s), 147.75 (s), 154.62 (d, 2J(P,C) =
2.2. X-ray measurements
X-ray data of compounds 1 and 2 were collected on a
Bruker SMART 1000 CCD single crystal diffractometer
with graphite monochromated MoKa radiation (k =
˚
0.71073 A). The structures were refined with SHELXL-97
[23] by full matrix least squares on F2. The positions of
hydrogen atoms were obtained from the difference Fourier
map. Routine Lorentz and polarization corrections were
applied and an absorption correction was performed using
the SADABS program for compound 2 [24].
1
4.1 Hz, Cipso). H NMR (d6-DMSO): 0.92–1.63 (m, 11H),
3
3
2.53 (d, J(P,H) = 10.7 Hz, 3 H, N-CH3), 6.84 (t, J(H,H) =
3
6.7 Hz, 2H, Ar-H), 7.01 (d, J(H,H) = 6.7 Hz, 2H, Ar-H),
3
2
7.60 (t, J(H,H) = 6.7 Hz, 2H, Ar-H), 8.07 (d, J(PNH) =
3
8.6 Hz, 2H, NH), 8.13 (d, J(H,H) = 6.7 Hz, 2H, Ar-H).
2.3. Computational details
IR (KBr, cmꢁ1): 3390 (m), 3145 (s), 2925 (s), 1588 (s),
1456 (s), 1394 (s), 1301 (s), 1264 (m), 1193 (s, mP@O),
1140 (s), 1006 (s), 978 (s), 924 (s), 810 (w), 770 (s), 640
(w), 540 (m), 499 (s).
Full geometry optimizations were performed for iso-
lated molecules 1 and 2 as well as for a compound
1:CH3OH pair, as observed in the crystal. Optimized struc-
tures were calculated by the density functional three-
parameter hybrid (DFT/B3LYP) and the Hartree–Fock
(HF) methods, using the 6-31G* basis set. Subsequently,
the harmonic frequencies were calculated at the same level
of approximation with the Gaussian98 program [25]. No
scale factor was used in the calculated frequencies.
3. Results and discussion
In this study, we prepared two new phosphoramidates
from the reaction of phenyl dichlorophosphate and N-
methylcyclohexyl phosphoramide dichloride intermediate
with the corresponding amines, respectively (Scheme 1).
Some characteristic spectroscopic data of these compounds
are given in Table 1. 1H NMR spectra of compounds 1 and
2.4. Syntheses
2
2 indicate J(P,H) coupling constants of 10.2 and 8.6 Hz,
2.4.1. N,N0-bis(cyclohexyl)-phenyl phosphoramidicacid
ester (1)
respectively. 3J(P,H) coupling constant (10.7 Hz) is
observed for the splitting of N-CH3 protons with phospho-
rus atom in 2, which is in agreement with our previously
reported values for related molecules [22]. 13C NMR spec-
trum of molecule 1 shows five signals for aliphatic cyclo-
hexyl groups. Two of them are doublet peaks with two
equal 3J(P,C) = 5.0 Hz. Therefore, the two CH2 carbon
atoms separated by three bond distances from phosphorus
To a stirred solution of phenyl dichlorophosphate
(1.05 g, 5 mmol) in dry acetonitrile (35 ml), a solution of
cyclohexylamine (1.98 g, 20 mmol) was added dropwise at
ꢁ5 ꢀC. After 12 h, the solvent was evaporated under vac-
uum and the oily product was washed with distilled water
and recrystallized from a mixture of CH3OH/H2O. Yield:

180
K. Gholivand et al. / Journal of Molecular Structure 874 (2008) 178–186
lattice. Here, the d(Hꢀ ꢀ ꢀA) distances for the hydrogen
O
P
bonding between solvent and phosphoramide molecule
˚
are shorter (1.90 and 1.86 A) than that of intermolecular
4 RNH2
+
˚
AP@Oꢀ ꢀ ꢀHAN hydrogen bond (2.03 A), probably due to
X
Cl
the strong interaction of small solvent molecule with
compound 1, than that between two phosphoramidates
molecules. Cameron et al. have been reported that the
co-crystallization of donor solvents (or arylammonium
chloride) in aryl derivatives precludes extended hydrogen
bonding networks [26]. On the other hand, compound 2
produces a one-dimensional polymeric chain from intermo-
lecular P(1)AO(1)ꢀ ꢀ ꢀH(1N)AN(1) hydrogen bonds (with
Cl
X = OC6H5,
R = C6H11
X = N(CH3)(C6H11), R = 2-C5H4N (2)
(1),
˚
d(Hꢀ ꢀ ꢀA) = 1.96 A) and also a weaker intramolecular
˚
N(2)ꢀ ꢀ ꢀH(3N)AN(3) hydrogen bond (d(Hꢀ ꢀ ꢀA) = 2.67 A).
O
P
The P@O bond lengths in molecules 1 and 2 are
˚
1.4877(15) and 1.4793(12) A, respectively, that are larger
˚
than the normal P@O bond length (1.45 A for P(O)Cl3)
+
2 RNH3Cl
[3]. In compound 2, the PANaromatic bond lengths are
longer than the PANaliphatic bond length because of the
interaction of Naromatic with p resonance system of 2-pyrid-
inyl ring results in a shorter CANaromatic bond length (the
CANaromatic bond lengths are shorter than the CANaliphatic
bond lengths). All of these PAN bonds are shorter than the
NHR
X
RHN
Scheme 1. Preparation pathway of compounds 1 and 2.
atom are not equivalent each other. The 13C NMR spec-
trum of 2 shows five signals for N-methylcyclohexyl moiety
with 2J(P,C) = 5.4 Hz (for N-methyl group) and
3J(P,C) = 2.4 Hz (for CH2 group). Also, 2,3J(P,C) coupling
constants for aromatic carbon atoms was obtained in these
molecules. The J(P,C) coupling constant observed for
˚
typical PAN single bond length (1.77 A for NaHPO3NH2
[3]). The nitrogen environments in the amidic groups are
nearly planar. In effect, for compound 1, the angles
C(7)AN(1)AP(1), P(1)AN(1)AH(1N) and C(7)AN(1)A
H(1N) have values of 125.2(2)ꢀ, 112.6(2)ꢀ and 118.4(2)ꢀ,
respectively with average 118.7ꢀ. Similarly, the sum of sur-
rounding angles around N(2) atom is 358.3ꢀ. Similar results
were obtained for the nitrogen atoms of structure 2, which
indicate sp2 hybridization for the nitrogen atoms (deviation
from the ideal value, 120ꢀ, may be caused by electronic
and/or steric effects).
The conformational space around the central phospho-
ric group of the molecule 1 has been studied using the
B3LYP/6-31G* level of theory. The molecular structure
determined in the X-ray diffraction study was used as the
initial structure for single point calculations for fixed values
of the O@PAN(2)AH(2N), O@PAN(1)AH(1N) and
O@PAO(2)AC(1) dihedral angles. For this purpose, the
SCAN option was used as implemented in the Gaussian
program [25], by varying each dihedral angle from 0ꢀ to
180ꢀ, in step of 30ꢀ. According to these calculations, the
most stable conformation is similar to the structure found
in the crystal. Chair and planar carbon skeleton were calcu-
lated for the cyclohexyl and phenyl rings, respectively.
Slight conformational differences, which are mainly
reflected in the values observed for dihedral angle around
compound 1 are as follow: J(P,C) = 6.4 Hz > 3J(P,C) =
2
4.9 Hz, whereas in compound 2, 2J(P,C) = 3J(P,C) =
4.1 Hz.
Single crystals of compounds 1 and 2 were obtained
from CH3OH/H2O solutions at room temperature. The
crystallographic data and the details of the X-ray analysis
are represented in Table 2, selected bond lengths and angles
for compounds 1 and 2 are given in Tables 3 and 4, respec-
tively. Hydrogen bonding data of these structures are pre-
sented in Table 5. Molecular structures are shown in Figs. 1
and 2, and unit cell packing in Figs. 3 and 4, for com-
pounds 1 and 2, respectively.
Compound 1 forms a centrosymmetric dimmer via two
equivalent
intermolecular
P(1)AO(1)ꢀ ꢀ ꢀH(2N)AN(2)
hydrogen bonds. Also, the O(1) and N(1) atoms of com-
pound 1 form intermolecular O(1)ꢀ ꢀ ꢀH(1O)AO(1S) and
O(1S)ꢀ ꢀ ꢀH(1N)AN(1) hydrogen bonds with solvent mole-
cule. Therefore, each dimmer is connected to four mole-
cules of CH3OH. Linking of these hydrogen bonds leads
to a one-dimensional polymeric chain in the crystalline
Table 1
Selected NMR spectroscopic data for compounds 1 and 2
Compound
d(31P)
d(N–1H)
d(13CH2)
2J(PH)
3J(PH)
3J(P,Caliphatic
)
2J(PCaromatic
)
3J(PCaromatic
)
(ppm)
(ppm)
(ppm)
(Hz)
(Hz)
(Hz)
(Hz)
(Hz)
1
2
10.81
3.66
4.49(dd)
8.07(d)
35.11(d), 35.22(d)
30.02(d)
10.2
8.6
–
10.7
5.0, 5.0
2.4, 5.4
6.4
4.1
4.9
4.1

K. Gholivand et al. / Journal of Molecular Structure 874 (2008) 178–186
181
Table 2
Crystallographic data for compounds 1 and 2
1
2
Empirical formula
Formula weight
Temperature (K)
C19H33N2O3P
368.44
120(2)
C17H24N5OP
345.38
120(2)
˚
Wavelength (A)
0.71073
0.71073
ꢀ
Crystal system, space group
Triclinic, P1
Monoclinic, P21/c
Unit cell dimensions
˚
a (A)
8.8679(16)
10.230(2)
12.511(2)
95.918(4)
103.948(4)
110.818(4)
1007.1(3)
2, 1.215
11.4760(7)
18.5607(12)
8.6227(6)
90.0
108.751(5)
90.0
˚
b (A)
˚
c (A)
a (ꢀ)
b (ꢀ)
c (ꢀ)
3
˚
V (A )
1739.2(2)
4, 1.319
Z, calculated density (Mg mꢁ3
)
Absorption coefficient (mmꢁ1
F(000)
)
0.156
400
0.173
736
Crystal size (mm)
h range for data collection (ꢀ)
0.25 · 0.20 · 0.05
2.18–28.09
0.20 · 0.20 · 0.15
1.87–30.01
Limiting indices
ꢁ11 6 h 6 10; ꢁ13 6 k 6 12; ꢁ16 6 l 6 15
ꢁ166h 6 15; ꢁ26 6 k 6 25; ꢁ12 6 l 6 12
20044/5034 [0.0552]
99.3
Semi-empirical from equivalents
0.9786 and 0.9633
Full-matrix least-squares on F2
5034/0/218
Reflections collected/unique [R(int)]
Completeness to h (%)
Absorption correction
Max. and min. transmission
Refinement method
Data/restraints/parameters
Goodness-of-fit on F2
Final R indices
7594/4829 [0.0345]
98.2
None
–
Full-matrix least-squares on F2
4829/0/227
0.837
1.065
R1 = 0.0489, wR2 = 0.0921
R1 = 0.1038, wR2 = 0.1069
0.313 and ꢁ0.279
R1 = 0.0496, wR2 = 0.0877
R1 = 0.0872, wR2 = 0.0945
0.397 and ꢁ0.449
R indices (all data)
Largest diff. peak and hole (e A
ꢁ3
˚
)
the PAN(2) and PAO(2) single bonds, are probably caused
by intermolecular interactions in the crystal. It is well
known that intermolecular interactions may cause the
molecular geometry in the solid phase to be different from
that of the free molecule.
and O@PAN(2), respectively. These values are well repro-
duced by quantum chemical calculations, where; obviously,
intermolecular hydrogen bonds are not present. Thus, the
difference in this bond angle seems to be related with
attractive intramolecular interactions between the
N(2)AH amide group and the P@O double bond. The
Full geometry optimizations of isolated molecules were
performed, also for a pair of compound 1:CH3OH mole-
cules interacting through N(1)AHꢀ ꢀ ꢀO(methanol) hydro-
gen bond. This model represents the fragment of a
chain in the crystal formed by molecules of compound 1
linked by hydrogen bond assisted by co-crystallization of
solvent molecules. Calculations have predicted the
N(1)AH(1N)ꢀ ꢀ ꢀO(1S) hydrogen bond length of about
˚
short non-bonded H(2N)ꢀ ꢀ ꢀO(1) distance (2.629 A) and
the nearly syn orientation of the P@O and the N(2)AH
bonds support this assumption [the O@PAN(2)H dihedral
angle is ꢁ28.1ꢀ in the crystal].
Calculations have revealed that the N(1)AH bond
involved in intermolecular hydrogen bonding is longer
˚
(by 0.012 A) than the N(2)AH bond. Thus, the two amine
˚
2.01 A, and the N(1)AH(IN)ꢀ ꢀ ꢀO(1S) bond angle of 159ꢀ,
groups for the compound 1 in the solid phase become non-
equivalent. In such a case, the presence of two bands are
expected in the characteristic amide stretching region,
which correspond to two different m(NAH) stretching
vibrations.
Table 6 gathers selected experimental and calculated fre-
quencies for compound 1. The simulated infrared spectrum
for the molecule 1 is given in Fig. 5. Two intense bands
appear in the IR spectrum at 1222 and 910 cmꢁ1 and are
assigned to the m(OAC) and m(OAP) stretching modes of
the phenoxyphosphorus moiety, respectively. These normal
modes are calculated at 1254 and 908 cmꢁ1, respectively.
The calculated P@O stretching vibration [m(P@O)] is pre-
dicted as an intense band at 1239 cmꢁ1, which correlates
˚
the N(1)ꢀ ꢀ ꢀO(1S) distance being 2.99 A. The experimentally
˚
determined N(1)ꢀ ꢀ ꢀO(1S) length is similar, 2.84 A, how-
ever, the N(1)AH(IN)ꢀ ꢀ ꢀO(1S) bond angle of 163.8ꢀ shows
less deviation from linearity than the calculated structure.
Table 3 compares calculated selected geometric parame-
ters with the experimental data. As follows from this com-
parison, the bond lengths and angles calculated for the
central phosphoric moiety show quite good agreement with
experiment. The geometric parameters of the diamide
phosphoric (ANH)2P@O groups are expected to be sensi-
tive to the formation of intermolecular hydrogen bonding
in crystal. This is reflected mainly in the O@PAN bond
angles, with values of 108.6ꢀ and 121.5ꢀ for O@PAN(1)

182
K. Gholivand et al. / Journal of Molecular Structure 874 (2008) 178–186
Table 3
a
˚
Selected experimental (X-ray) and calculated geometrical parameters for compound 1 (bond lengths in A, bond angles in ꢀ)
Parameter
X-ray
HF/6-31G*
B3LYP/6-31G*
B3LYP/6-31G*b
P(1)AO(1)
P(1)AO(2)
P(1)AN(1)
P(1)AN(2)
O(2)AC(1)
N(1)AC(7)
N(2)AC(13)
N(1)AH(1N)
N(1)AH(2N)
C(1)AC(2)
C(1)AC(6)
C(2)AC(3)
1.4877(15)
1.6021(15)
1.6160(16)
1.6160(17)
1.385(2)
1.472(2)
1.470(3)
0.967
1.460
1.610
1.650
1.630
1.370
1.460
1.450
0.991
0.990
1.380
1.380
1.380
1.490
1.650
1.670
1.660
1.380
1.470
1.460
1.010
1.010
1.398
1.398
1.398
1.489
1.671
1.662
1.654
1.389
1.471
1.459
1.003
0.990
1.385
1.385
1.385
0.926
1.379(3)
1.385(3)
1.387(3)
O(1)AP(1)AN(1)
O(1)AP(1)AN(2)
O(1)AP(1)AO(2)
N(1)AP(1)AN(2)
N(1)AP(1)AO(2)
N(2)AP(1)AO(2)
P(1)AO(2)AC(1)
P(1)AN(1)AC(7)
P(1)AN(2)AC(13)
P(1)AN(2)AH(2N)
P(1)AN(1)AH(1N)
C(7)AN(1)AH(1N)
C(13)AN(2)AH(2N)
C(2)AC(1)AO(2)
C(6)AC(1)AO(2)
C(2)AC(1)AC(6)
O(1)AP(1)AN(2)AH(N2)
121.55(9)
108.62(9)
110.72(8)
106.84(9)
96.26(8)
112.43(9)
127.24(14)
125.24(15)
127.25(15)
116.9
112.6
118.4
114.1
124.1(2)
115.59(19)
120.28(15)
ꢁ28.1
119.6
109.7
114.7
106.8
95.7
121.2
110.3
115.1
104.5
94.9
122.0
110.1
113.6
105.6
95.3
109.2
126.6
121.4
128.3
113.6
113.9
116.7
114.2
122.4
116.6
120.9
ꢁ11.0
110.0
125.4
120.4
127.4
112.3
112.6
115.8
113.5
123.2
116.0
120.8
ꢁ17.3
109.0
122.7
119.5
127.9
113.8
114.4
116.8
114.0
112.1
116.9
121.0
ꢁ15.6
O(1)AP(1)AN(1)AH(1N)
O(1)AP(1)AOAC(1)
87.7
43.8
94.9
50.4
88.3
45.6
91.9
52.7
a
For atom numbering, see Fig. 1.
Calculated parameters for the compound 1:CH3OH pair.
b
well with the observed band at 1199 cmꢁ1 in the IR spec-
trum of solid (1), and with reported data for similar substi-
tuted phosphate species [22]. The characteristic
phosphoramidate m(PAN) stretching modes are predicted
at 1008 cmꢁ1 [m(PAN1)] and 1026 cmꢁ1 [m(PAN2)], fre-
quency values that are in good agreement with the band
observed at 1021 cmꢁ1 in the IR spectrum. The m(NAC)
stretching modes for the amide groups are predicted as
strong intensity bands, which differ slightly in their wave-
numbers [1115 and 1126 cmꢁ1 for the m(N1AC7) and
m(N2AC13) modes, respectively]. In the experimental spec-
trum this region is dominated by a strong absorption can-
tered at 1099 cmꢁ1. The amide deformation modes are
assigned to the bands at 1484 and 1439 cmꢁ1 in the IR
spectrum of solid (1), taking into account calculated values
at 1471 and 1462 cmꢁ1 for the d(N2AH) and d(N1AH),
respectively. It is well known that the d(NAH) overtone
is generally observed in the IR spectra of amidates, because
its intensity could be reinforced by the Fermi resonance
effect with the NAH fundamental stretching mode [27].
For compound (1), the strong band at 2920 cmꢁ1 was
assigned to this overtone mode. In both experimental and
simulated spectra, complicated pattern of absorptions were
observed in the regions between 1200–1650 and 3000–
3250 cmꢁ1, which originate from the diverse CAH stretch-
ing and deformation modes, respectively. Frequency calcu-
lations were done also for the molecule 1:CH3OH
aggregate. Main differences are reflected in the m(N1AH)
stretching mode. In effect, while slight changes are calcu-
lated for the m(N2AH) band location (7 cmꢁ1), an impor-
tant red shift (135 cmꢁ1) is predicted for the m(N1AH),
together with an important enhancement in the band inten-
sity with respect to the isolated molecule. These are the
expected behavior for stretching modes which are directly
involved in hydrogen bond interactions [28]. The high fre-
quency region of the IR spectrum of solid (1) shows the
presence of a band with medium intensity at 3230 cmꢁ1
,
which could be related with the m(NAH) mode for the
interacting N1AH amidate moiety.
Selected optimized geometrical parameters for com-
pound (2) are listed in Table 6 and compared with the
X-ray experimental data. The global conformation of the
molecule 2 seems to be similar in both the solid and gas-
eous phases, since quite similar values are observed when
experimental and calculated dihedral angles are compared.
Chair and planar skeleton were calculated for the

K. Gholivand et al. / Journal of Molecular Structure 874 (2008) 178–186
183
Table 4
Selected experimental (X-ray) and calculated geometrical parameters for
a
˚
compound 2 (bond lengths in A, bond angles in ꢀ)
X-ray
HF/6-31G*
B3LYP/6-31G*
P(1)AO(1)
P(1)AN(5)
P(1)AN(1)
P(1)AN(3)
N(3)AC(6)
N(1)AC(1)
N(2)AC(1)
N(2)AC(2)
N(3)AC(6)
N(4)AC(6)
N(4)AC(7)
N(5)AC(11)
N(5)A(C12)
N(2)ꢀ ꢀ ꢀN(3)
1.4793(12)
1.6386(15)
1.6587(15)
1.6617(15)
1.396(2)
1.397(2)
1.332(2)
1.350(2)
1.396(2)
1.342(2)
1.349(2)
1.465(2)
1.485(2)
2.995
1.460
1.653
1.694
1.665
1.471
1.457
1.323
1.375
1.400
1.324
1.393
1.471
1.471
2.973
1.489
1.670
1.730
1.680
1.400
1.390
1.331
1.340
1.391
1.330
1.341
1.460
1.480
2.830
O(1)AP(1)AN(1)
O(1)AP(1)AN(3)
O(1)AP(1)AN(5)
N(5)AP(1)AN(1)
N(5)AP(1)AN(3)
N(1)AP(1)AN(3)
P(1)AN(5)AC(11)
P(1)AN(5)AC(12)
C(11)AN(5)AC(12)
P(1)AN(1)AC(1)
P(1)AN(3)AC(6)
C(1)AN(2)AC(2)
C(1)AN(1)AH(N1)
P(1)AN(1)AH(1N)
C(1)AN(2)AC(2)
C(6)AN(4)AC(7)
115.13(8)
114.71(7)
111.45(7)
107.29(8)
105.65(8)
101.70(8)
119.44(12)
119.69(12)
117.31(14)
125.66(13)
129.23(13)
116.76(16)
114.6
116.5
116.6
111.7
106.4
102.
115.7
118.7
111.7
106.5
103.1
99.4
119.7
119.4
118.6
129.4
126.8
118.5
113.4
113.4
118.4
117.9
Fig. 1. Ortep view of compound 1, C6H5OP(O)(NHC6H11)2, with 50%
probability ellipsoids.
99.6
120.1
121.0
118.5
128.0
127.8
118.6
112.9
115.2
119.0
118.5
119.6
116.76(16)
117.1(2)
O(1)AP(1)AN(5)AC(11)
O(1)AP(1)AN(5)AC(12)
O(1)AP(1)AN(1)AC(1)
O(1)AP(1)AN(3)AC(6)
P(1)AN(1)AC(1)AN(2)
P(1)AN(3)AC(6)AN(4)
a
171.9
230.0
61.4
49.7
7.5
170.1
4.5
64.2
48.8.
37.0
ꢁ179.5
179.9
17.5
75.7
50.6
32.8
ꢁ171.4
ꢁ161.3
For atom numbering, see Fig. 3.
cyclohexyl and 2-pyridinyl rings, respectively. Similar geo-
metric parameters are obtained by both HF and B3LYP
applied methods. These results are in agreement with the
experimental values obtained from the X-ray analysis,
again taking into account that theoretical calculations were
performed for the molecule isolated in vacuum. Differences
in the bond lengths and in bond angles are smaller than ca.
Fig. 2. Unit cell packing of compound 1, C6H5OP(O)(NHC6H11)2, along
a axis.
lengths corresponds to the PAN(5) bond in both HF and
DFT methods. The largest differences between experimen-
tal and calculated angle values are 4.0ꢀ and 3.8ꢀ for
O@PAN(3) and PAN(3)AC(6) in B3LYP/6-31G* method.
˚
0.07 A and 4ꢀ, respectively. The considerable differences
between the calculated and experimental data of the bond
Table 5
˚
Hydrogen bonds for compounds 1 and 2 (distances in A and angles in ꢀ)
Compound
d(Hꢀ ꢀ ꢀA)
d(DAH)
d(Hꢀ ꢀ ꢀA)
\DHA
d(Dꢀ ꢀ ꢀA)
1
N(1)AH(1N)ꢀ ꢀ ꢀO(1S)
0.97
0.87
0.93
1.90
1.86
2.03
164.0
169.0
170.0
2.843(3)
2.721(2)
2.943(2)
O(1S)AH(1O)ꢀ ꢀ ꢀO(1) [ꢁx + 1, ꢁy, ꢁz]
N(2)AH(2N)ꢀ ꢀ ꢀO(1) [ꢁx, ꢁy, ꢁz]
2
N(1)AH(1N)ꢀ ꢀ ꢀO(1) [x, ꢁy + 1/2, z ꢁ 1/2]
0.94
0.92
1.96
2.67
164.0
101.6
2.871(2)
2.995(2)
N(3)AH(3N)ꢀ ꢀ ꢀN(2)

184
K. Gholivand et al. / Journal of Molecular Structure 874 (2008) 178–186
Table 6
Selected experimental (KBr pellets) and calculated (B3LYP/6-31G*)
frequencies (cmꢁ1) for compounds 1 and 2
Mode
Compound 1
Compound 2
Experimental Calculated
Experimental Calculated
m(NAH)a 3230
3578
3390
3575
m(N2AH)
3548
m(N1AH)
3368
3145
m(N1AH)
m(N3AH)
d(NAH)b 1484
1471
d(N2AH)
1462
1588
1456
1499
1439
1495
d(N1AH)
1394
1301
1458
1431
m(P@O)
m(OAC)
m(OAP)
1199
1222
910
1239
1254
908
1115
1193
1269
m(NAC)b 1099
Fig. 3. Ortep view of compound 2, [N(CH3)(C6H11)]P(O)(2-C5H4N-NH)2,
with 50% probability ellipsoids.
m(N1AC7)
1126
m(N2AC13)
m(PAN)
1021
1026 m(PAN2)
1008 m(PAN1)
978
924
810
985
m(PAN5)
949
m(PAN3)
890
m(PAN1)
a
For the compound (1):CH3OH pair, calculated m(N2AH) and
m(N1AH) values are 3585 and 3413 cmꢁ1, respectively.
b
d(NAH) and m(NAC) normal modes are strongly coupled in com-
pound (2), see text.
between the two m(NAC) stretching modes and the two
d(NAH) amide deformation modes. These modes are
observed in the IR spectra of solid (2) as four absorption
bands with strong intensity, which are observed at 1588,
1456, 1394 and 1301 cmꢁ1. As in the previous case, a strong
absorption at 2925 cmꢁ1 can be assigned to the overtone
associated with the d(NAH) amide deformation mode.
The characteristic P@O stretching vibration is predicted
as a band of medium intensity located at 1269 cmꢁ1, which
correlated very well with the experimental value at
1193 cmꢁ1. The m(PAN) stretching modes appear at 978,
924 and 810 cmꢁ1 in the IR spectrum, which were assigned
as m(PAN5), m(PAN3) and m(PAN1), respectively (see
Table 6). As in the previous spectrum, the complicated pat-
tern of absorption in the regions of 1200–1650 and 3000–
3250 cmꢁ1 originates from the diverse CAH stretching
and deformation modes, respectively. It is worthy to note
the feature observed in the high-wavenumber region of
the calculated spectrum. The highest normal mode of
vibration corresponds to the m(N1AH) stretching, which
is calculated at 3575 cmꢁ1 and posses a weak intensity.
On the other hand, m(N3AH) normal mode is assigned to
the very intense absorption located at 3368 cmꢁ1, reflecting
the occurrence of N(2)ꢀ ꢀ ꢀHAN(3) intramolecular hydrogen
bond interaction [27]. These modes appear at 3390 and
Fig. 4. Unit cell packing of compound 2, [N(CH3)(C6H11)]P(O)(2-C5H4N-
NH)2.
Analogous differences for the HF/6-31G* calculations are
1.9ꢀ and 2.4ꢀ, respectively.
The intramolecular hydrogen bond interaction between
one amide group and a nitrogen atom in the 2-pyridinyl
ring [N(3)AHꢀ ꢀ ꢀN(2)] is well reproduced by quantum
chemical calculations. The calculated values for the
O@PANC dihedral angles are very close to the experimen-
tal ones, and the experimentally found N(2)ꢀ ꢀ ꢀN(3) non-
˚
˚
bonded distance (2.995 A) accords well with the calculated
values (2.973 and 2.830 A for the HF and B3LYP methods,
respectively).
Table 6 gathers selected experimental and calculated fre-
quencies for compound 2, while the simulated infrared
spectrum is given in Fig. 6. A group of four bands with
high intensities, which appear at 1499, 1495 and 1458,
1431 cmꢁ1 are assigned as coupled modes of vibrations

K. Gholivand et al. / Journal of Molecular Structure 874 (2008) 178–186
185
31P NMR spectra show that d(31P) in compound 1
occurs at down field relative to that of 2. IR spectra
revealed that the m(P@O) stretching mode for compound
1 appears at 1199 cmꢁ1, while for compound 2 this mode
is assigned to a strong intensity band at 1193 cmꢁ1. These
observations indicate that the substituents at the phospho-
rus atom in compound 1 are more electron withdrawing
than in compound 2 resulting in a more deshielded P atom
and a stronger P@O bond. A noticeable contradiction in
the trend of both frequencies of the P@O stretching normal
mode of vibration for 1 and 2 and corresponding bond
distances results apparent. Thus, whereas the experimental
frequencies for 1 and 2 are 1199 and 1193 cmꢁ1 the corre-
12
10
8
6
4
2
˚
sponding bond distances are 1.4877(15) and 1.4793(12) A,
0
respectively. A close analysis of these normal modes of
vibration for 1 and 2 reveals a high degree of mixture being
the normal coordinate not only based on the P@O but
also on the OAC and NAC internal coordinates of the
methoxyphenyl and the 2-pyridinyl rings for 1 and 2,
respectively.
4000
3500
3000
2500
2000
1500
1000
500
Wavenumbers [cm-1]
Fig. 5. Simulated infrared spectrum for compound 1 from B3LYP/6-31G*
calculation.
5. Supplementary data
16
14
12
10
8
Crystallographic data for the structures 1 and 2 in this
paper have been deposited with Cambridge Crystallo-
graphic Data Center as supplementary publication nos.
CCDC 601411 (C19H33N2O3P) and CCDC 601410
(C17H24N5OP). Copies of the data may be obtained, free
of charge, on application to CCDC, 12 Union Road,
Cambridge CB2 1EZ, UK (fax: +44 1223 336033; e-mail:
deposit@ccdc.cam.ac.uk or http://www.ccdc.cam.ac.uk).
6
4
Acknowledgements
2
Financial support by the Research Council of Tarbiat
Modarres University, Volkswagen-Stiftung and the Deut-
sche Forschungsgemeinschaft is gratefully acknowledged.
The Argentinean authors thank the Consejo Nacional de
0
4000
3500
3000
2500
2000
1500
1000
500
Wavenumber [cm-1]
´
´
Investigaciones Cientıficas y Tecnicas (CONICET), the
Fig. 6. Simulated infrared spectrum for compound 2 from B3LYP/6-31G*
calculation.
´
´
Comision de Investigaciones Cientıficas de la Provincia
de Buenos Aires (CIC), the Facultad de Ciencias Exactas,
Universidad Nacional de La Plata, Repu´blica Argentina
for financial support. CODV especially acknowledges the
DAAD for its generous sponsorship of the DAAD
Regional Program of Chemistry of the Republic of Argen-
tina (supporting Latin-American students for a PhD pro-
gram in La Plata). The authors acknowledge
Supercomputer Centre of the Secretary for the Technology,
3145 cmꢁ1 in the IR spectrum of solid (2) as a medium and
strong absorption, respectively.
4. Conclusions
Two new phosphoramidates were synthesized and char-
acterized by multinuclear NMR, IR spectroscopy and ele-
mental analyses. The crystal structures of these compounds
were determined using X-ray crystallography. Compound
1 forms a centrosymmetric dimmer via two equal intermo-
lecular P@Oꢀ ꢀ ꢀHAN hydrogen bonds. Compound 2 crys-
Science and Productive Innovation (SECyT), Republica
Argentina, for computational time at the Clementina II
computer.
´
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tallizes forming
a one-dimensional polymeric chain
through intermolecular P@Oꢀ ꢀ ꢀHAN hydrogen bonds,
while weaker intramolecular Nꢀ ꢀ ꢀHAN hydrogen bond
has been also observed.
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