Synthesis, characterisation, conformational preferences, dynamic NMR studies and antimicrobial evaluation of N-nitroso- and N-formyl-c-3,t-3-dimethyl-r-2,c-7-diphenyl-1,4-diazepan-5-ones

Article abstract of DOI:10.1016/j.molstruc.2016.01.023

The stereochemical preferences of N-nitroso- and N-formyl-c-3,t-3-dimethyl-r-2,c-7-diphenyl-1,4-diazepan-5-ones 3 & 4, respectively, have been determined using 1D and 2D NMR spectral techniques. Interestingly, the N-nitroso compound 3 is found to prefer a

Full text of DOI:10.1016/j.molstruc.2016.01.023

Accepted Manuscript
Synthesis, characterisation, conformational preferences, dynamic NMR studies
and antimicrobial evaluation of N-nitroso- and N-formyl-c-3, t-3-dimethyl-r-2,c-7-
diphenyl-1,4-diazepan-5-ones
S. Ponnuswamy, A. Akila, D. Kiruthiga devi, V. Maheshwaran, M.N. Ponnuswamy
PII:
S0022-2860(16)30023-0
10.1016/j.molstruc.2016.01.023
MOLSTR 22139
DOI:
Reference:
To appear in: Journal of Molecular Structure
Received Date: 10 October 2015
Revised Date: 12 January 2016
Accepted Date: 12 January 2016
Please cite this article as: S. Ponnuswamy, A. Akila, D. Kiruthiga devi, V. Maheshwaran, M.N.
Ponnuswamy, Synthesis, characterisation, conformational preferences, dynamic NMR studies and
antimicrobial evaluation of N-nitroso- and N-formyl-c-3, t-3-dimethyl-r-2,c-7-diphenyl-1,4-diazepan-5-
ones, Journal of Molecular Structure (2016), doi: 10.1016/j.molstruc.2016.01.023.
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Graphical Abstract

ACCEPTED MANUSCRIPT
Synthesis, characterisation, conformational preferences, dynamic NMR
studies and antimicrobial evaluation of N-nitroso- and N-formyl-c-3,t-3-
dimethyl-r-2,c-7-diphenyl-1,4-diazepan-5-ones
a
a
a
b
b
S. Ponnuswamy *, A. Akila , D. Kiruthiga devi , V. Maheshwaran , M. N. Ponnuswamy
a
P G. & Research Department of Chemistry, Government Arts College (Autonomous), Coimbatore 641 018, Tamil Nadu, India.
b
Centre of Advanced study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, Tamil Nadu,
India.
*
corresponding author. E-mail address : kspons2001@gmail.com
Mobile number : +919244645744
Abstract
The stereochemical preferences of N-nitroso- and N-formyl-c-3,t-3-dimethyl-r-
,c-7-diphenyl-1,4-diazepan-5-ones 3 & 4, respectively, have been determined using 1D
2
and 2D NMR spectral techniques. Interestingly, the N-nitroso compound 3 is found to
prefer an equilibrium between alternate chair conformations with diaxial phenyl groups,
while the N-formyl compound 4 prefers flattened boat conformation.
This is
stereochemically a novel report on the flexible rings adopting a chair conformation with
diaxial phenyl groups. The X-ray crystal structure of N-nitroso-c-3,t-3-dimethyl-r-2,c-7-
diphenyl-1,4-diazepan-5-one (3) also supports the chair conformation with diaxial phenyl
1
groups. Dynamic H NMR spectral studies have been carried out on the N-nitroso and N-
formyl diazepan-5-ones 3 & 4 and the energy barriers for N-NO and N-CO rotations are
found to be 88.7 and 75.7 kJ/mol, respectively. The antimicrobial activities have been
determined for the compounds 2-4 and it is found that all the compounds exhibit
significant antibacterial and antifungal activities when compared to the standard
chloramphenicol.
Keywords: c-3,t-3-dimethyl-r-2,c-7-diphenyl-1,4-diazepan-5-one, NMR spectra, Dynamic
NMR, alternate chair, flattened boat, N-nitroso, N-formyl diazepan-5-one.
1

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1
. Introduction
The conformational preferences of N-nitroso-r-2,c-6-diphenylpiperidin-4-
ones and piperidines [1-3], N-nitroso-3-azabicyclo[3.3.1]nonanes [4-6], N-nitroso and N-
1
4
formyl diazepans [7-9], N, N-dinitroso diazepans [9,10], N-ethoxycarbonyl & N-phenyl
carbamoyl diazepans [11] and N-formyl piperidin-4-ones and piperidines [12] have been
studied. Most of the N-nitroso- and N-formyl-r-2,c-6-diphenylpiperidines [1-3, 12] are
found to prefer either twist-chair, twist-boat (or) flattened boat conformation with high
energy barrier around 70-80 kJ/mol. However, a very few N-nitroso piperidines prefer to
adopt an alternate chair conformation with diaxial phenyl groups [2,3,12c]. The N-nitroso
and N-formyl derivatives of diazepans [7-9] are found to prefer flattened boat conformation
and exist in an equilibrium between syn and anti rotamers at room temperature with
coplanar orientation. The delocalization of nitrogen lone pair into the double bonds of the
N-N=O and N-C=O systems results in restricted rotation about the N-N and N-C bonds,
1
,3
respectively [13]. The energy barrier for these N-N and N-C rotations is controlled by A -
strain (allylic strain) [14,15]. The steric interaction between the coplanar nitroso & formyl
groups and the α-substituents tends to destabilize the chair conformation with diequatorial
phenyl groups. In order to relieve the allylic strain, the molecule may flip over to other
conformation. The reported dinitroso diazepans derivatives [9-10] prefer twist-chair
conformation while bisethoxycarbonyl derivatives of diazepans prefer flattened boat
conformation and mono ethoxycarbonyl compound prefers the chair conformation with
endo orientation of carbethoxy group [11b].
Though the stereochemistry of N-nitroso and N-formyl derivatives of a few
diazepans was reported earlier, no work has been done on c-3,t-3-dimethyl-1,4-diazepan-
2

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3
5-one. In order to check the effect of additional axial methyl group at C , over the
conformational preferences of diazepan ring, the N-nitroso- and N-formyl-c-3,t-3-dimethyl-
r-2,c-7-diphenyl-1,4-diazepan-5-ones 3 & 4, respectively, have been synthesized.
Surprisingly, it is found that N-nitroso-diazepan-5-one 3 adopts alternate chair
conformation with diaxial phenyl groups in solution as well as in solid states. However, N-
formyl-diazepan-5-one 4 is found to prefer flattened boat conformation with quasi axial
phenyl groups in solution state. Thus, the introduction of N-nitroso and N-formyl groups
exerts a large influence on the conformation of the ring and orientation of the substituents.
2. Experimental
2.1 Materials, methods and instruments
All the reported melting points were taken in open capillaries and are uncorrected.
IR spectra were recorded in BRUCKER FT-IR alpha model spectrometer using KBr
1
13
3
pellets. The H and C NMR spectra were recorded in CDCl solution using TMS as the
internal standard in Bruker AMX 400 & 100 MHz NMR Spectrometer, respectively. 0.05 M
Solutions of the sample prepared in CDCl were used for recording 2D NMR spectra. The
3
tubes used for recording NMR spectra are of 5 mm diameter. Electron impact mass
spectra were recorded in JEOL GS mate spectrometer and microanalyses were
performed on Carlo Erba 1108 CHN analyser. Unless otherwise stated, all the reagents
and solvents used were of high grade and purchased from Sigma-Aldrich chemicals,
Bangalore, India and Merck chemicals, Worli, Mumbai. All the solvents were distilled prior
to use. The parent 3,3-dimethyl-2,7-diphenyl-1,4-diazepan-5-one 2 was prepared by
following the literature method [16].
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2.2 N-Nitroso-c-3,t-3-dimethyl-r-2,c-7-diphenyl-1,4-diazepan-5-one (3)
A mixture of c-3,t-3-dimethyl-r-2,c-7-diphenyl-1,4-diazepan-5-one (2, 1.3 g, 4
mmol) and conc. HCl (0.8 mL) was dissolved in 1:1 ethanol-water mixture (26mL). While
stirring, a solution of NaNO (0.42 g, 6 mmol) in 1:1 ethanol-water mixture (25 mL) was
added dropwise over a period of 30 min at RT. The stirring was continued for another
hrs. The crude product was purified by crystallisation from ethanol. The analytical data
of the compound 3 are furnished in Table-1.
2
2
2.3 N-Formyl-c-3,t-3-dimethyl-r-2,c-7-diphenyl-1,4-diazepan-5-one (4)
An ice cold solution of acetic-formic anhydride was prepared from acetic anhydride
(
10 ml), and 85% of formic acid (5 ml) and this solution was slowly added to cold solution
of c-3,t-3-dimethyl-r-2,c-7-diphenyl-1,4-diazepan-5-one (2,1.47g, 5mmol) in anhydrous
benzene. The reaction mixture was stirred at room temperature for 5hrs. The organic
layer was separated, dried over anhydrous Na
2
SO
4
and concentrated
.
The resulting
product was purified by crystallisation from ethanol. The analytical data of the compound
4
are furnished in Table-1.
2.4 Structure determination and refinement
A single crystal of the N-nitroso-c-3,t-3-dimethyl-r-2,c-7-diphenyl-1,4-
diazepan-5-one (3) was mounted on a Bruker Kappa APEX II area-detector diffractometer
equipped with MoKα (0.71073 Å) radiation [17]. X-ray intensity data were collected for the
compound at room temperature (293 K). The data reduction and the absorption
corrections were carried out using SAINT and SADABS programs [18]. The structures
were solved by direct methods using the program SHELXS97 [19]. All the non-hydrogen
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2
atoms were refined anisotropically by full-matrix least-squares procedure on F taking all
the unique reflections using SHELXL97 [19]. The hydrogen atoms attached with carbon
atoms were placed in their calculated positions and included in the isotropic refinement
2 3
using the riding model with C–H= 0.93 Å (−CH) or 0.97 Å (−CH ) Å or 0.96 Å (−CH ) Å
with Uiso (H) = 1.2Ueq (parent C atom). The least-squares planes, geometrical and
puckering parameters of both the compounds were calculated using PLATON software
package [20].
3. Results and Discussion
The diazepan-5-one [16]
2
was prepared from c-3,t-3-dimethyl-r-2,c-6-
diphenylpiperidin-4-one 1a [1b] after converting to its hydrochloride 1b. The N-nitroso-c-
3,t-3-dimethyl-r-2,c-7-diphenyl-1,4-diazepan-5-one (3) was prepared from diazepan-5-one
2
by using sodium nitrite and HCl in an ethanol-water mixture (Scheme-1). The N-formyl-
c-3,t-3-dimethyl-r-2,c-7-diphenyl-1,4-diazepan-5-one (4) was prepared by the formylation
of diazepan-5-one 2 using acetic anhydride and formic acid (Scheme-1).
The IR spectra of the compounds 3 & 4 show the presence of amide >C
5
=O and
-1
-1
N
4
-H stretching bands at 1658 & 1672 cm and 3197 & 3244 cm , respectively. The
-1
absence of amine NH stretching band at 3280 cm and the presence of additional NO
-1
-1
(
1496 cm ) & CO (1638 cm ) stretching bands for the compounds 3 & 4, respectively,
when compared with the parent diazepan-5-one 2, confirm the formation of nitroso and
formyl derivatives 3 and 4. Furthermore, the absence of Bohlmann bands [21] in the
-1
region 2700-2800 cm in both the compounds 3 and 4 indicates that either the nitrogen
lone pair is not antiperiplanar to the two α-hydrogens or the lone pair might be involved in
delocalization with the nitroso and formyl groups.
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3.1 Orientation of N-X=Y group
The N-X=Y groups can adopt either coplanar or perpendicular orientation to the
dynamically averaged plane of the ring. Doubling of proton and carbon NMR spectral
signals of 3 & 4 indicates that the N-X=Y functions adopt coplanar orientation and
delocalization of the lone pair of electrons on nitrogen of the compounds 3 & 4 into the
carbonyl & nitroso π-cloud is sufficient to create a substantial double bond character along
N-X=Y bond. This non-equivalence arises due to the syn and anti orientations of the N-
X=Y group. The syn rotamer refers to the rotamer in which N-X=Y function orients
towards C carbon and anti rotamer refers to the one in which N-X=Y function is away
2
2 7
from C carbon (towards C carbon, Figure-1). The anisochronous nature of proton and
carbon signals appearing at RT eliminates the possibility of perpendicular orientation.
Hence the N-N=O and N-C=O groups prefer to adopt coplanar orientation and it is further
confirmed from the following observations:
(
i) Greater deshielding of benzylic protons [22-24] compared to that of the parent
1
diazepan-5-one 2 in the H NMR spectra (Table-2).
1
3
(
ii) Greater shielding of C and C benzylic carbons [23,25-28] in C NMR spectra
2 7
(Table-3).
1
13
3
.2 Assignment of H and C NMR spectra
HSQC spectra of 3 & 4 have been used for the unambiguous assignment of syn
and anti NMR signals. This method is based on the observation that the carbons syn to
the –X=Y functions in compounds containing N-X=Y functions, such as N-NO, N-CHO and
6

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N-COR are always more shielded than anti carbons in their coplanar orientation. The
greater shielding of syn carbon shows,
(
(
i) steric strain over the syn α carbon as a result of the γ-eclipsed conformation of the
N-O bond with respect to syn C-N bond and
1 2 7 6
ii) partial eclipsing interactions between the N -C and C -C bonds due to the small
2
dihedral angle arising out of the sp hybri iz tion a hi ved by the ring nitrogen,due
d
a
c
e
to lone-pair delocalization in the coplanar orientation.
The β-carbon and the ipso carbon signals of both syn and anti rotamers experience
shielding effect compared to the parent compound 2 (Table-3). This may be due to the
decrease in dihedral angle between N(O)-N -C and N -C -C , C -N -C and N -C -C .
1
2
1
2
ipso
2
1
7
1
7
6
1
13
This fact has been used to assign the H & C NMR spectral signals due to syn and anti
2
rotamers. When compared to the parent compound 2 (Table-3), the C carbon syn to the
nitroso group is shielded by about 15.7 ppm, whereas the chemical shift of anti carbon is
not affected much.
1
3
In the C NMR spectrum of 3, between two benzylic carbon signals (i.e: 58.2, &
7
3.8) the more shielded signal at 58.2 is assigned to the C carbon of the syn rotamer (C
2
2
2
syn to the C=O) and the signal at 73.8 is assigned to the C carbon of the anti rotamer (C
2
anti to the C=O). These two carbon signals at 58.2 & 73.8 correlate with the benzylic
protons at 5.99 and 6.52 ppm, respectively, in the HSQC spectrum. Hence, the signal at
2 2
5.99 is assigned to H of syn rotamer and 6.52 is assigned to H of anti rotamer. The
other carbon and proton signals are assigned using DEPT, COSY and HSQC NMR
spectra based on benzylic carbon and proton signals.
7

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The signals at 6.42 & 6.63 ppm appearing as triplet and singlet are assigned to the
H
7
protons of syn & anti rotamers, respectively. From the COSY spectrum, the signal at
6
.42 has correlation with 3.49 & 3.62 ppm and the other signal at 6.63 has correlation with
the signals at 2.98 & 3.34. Hence the peaks at 3.49 & 3.62 and 2.98 & 3.34 are assigned
to C protons (axial & equatorial) of syn and anti rotamers, respectively. The W-coupling
between H and amide N-H is observed with a coupling constant value of 1.6 Hz. Similar
6
6
e
procedure has also been applied for the assignment of NMR spectral signals of compound
4.
In the case of 4, the signals for benzylic proton at C appearing as two singlets at
2
5.90 and 4.41 ppm are assigned to syn & anti rotamers, respectively (Figure-2). The
signals at 5.05 & 6.25 ppm appearing as triplets are assigned to the H protons of syn &
7
anti rotamers, respectively. The peaks at 3.44 & 3.23 and 3.26 & 3.37 ppm, are due to C6
(
axial & equatorial) protons of syn and anti rotamers, respectively. Based on the DEPT
spectrum, the signals at 173.5 & 173.2 for 3 and 174.2 & 173.2 for 4 are assigned to the
amide >C=O at C of syn & anti rotamers, respectively (Figures-3 & 4).
In the parent diazepan-5-ones 2, the coupling constant between H
5
7
& H6e protons is
zero indicating that the dihedral angle is close to 90° [7]. However, in the case of N-
nitroso- and N-formyl-1,4-diazepan-5-ones 3 & 4, coupling constant values are found to be
2.4 & 4.8 Hz and 3.5 & 5.5 Hz, respectively. This increase in coupling constant from zero,
suggests a decrease in the dihedral angle from 90° between H & H protons. The cis
7
6e
and trans dihedral angles are estimated to be 64°& 56°for the nitroso compound 3 and
8°& 158°for formyl compound 4, respectively, using DAERM [29]. The aromatic protons
appear as multiplet between 7.26-6.69 ppm. The peak at 1.73 ppm is assigned to amide
N-H based on the D O exchange studies.
3
2
8

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3.3. Preferred conformations: Conformation of N-nitroso-c-3,t-3-dimethyl-r-2,c-7-diphenyl-1,4-
diazepan-5-one (3)
The vicinal coupling constants and the dihedral angles show that the parent diazepan-
5-one 2 prefers to exist in a chair conformation [16] (Figure-5).
Possible conformations of N-nitroso- and N-formyl-1,4-diazepan-5-ones are depicted
in Figure-6
(
(
(
(
(
i)
Chair conformation with equatorial phenyl groups (IA & IB)
Chair conformation with axial phenyl groups (IIA & IIB)
Twist-chair conformation (IIIA & IIIB)
ii)
iii)
iv)
v)
Twist-boat conformation (IVA & IVB)
Boat-conformation (VA & VB)
The chair conformation IA and IB with equatorial phenyl groups is destabilized by
1,3
A -strain. The chair form requires a cis dihedral angle of 60 °. The calculated dihedral
angles of 3 (64° & 56°) eliminate the possibility of chair con formation IA & IB.
7
Furthermore, in the chair conformation, the C benzylic proton is in trans relationship with
the axial proton at C and the expected coupling constant between the benzylic and
6
methylene protons would be J7a,6a = 10.0-12.0 Hz, J7a,6e = 2.0-4.0 Hz. However, the
observed coupling constants of 3 are J7a,6a = 4.8 Hz and J7a,6e = 2.4Hz (Table-4). Hence
this conformation has become unfavorable and ring could flip into another chair
conformation.
1
,3
In the twist-chair conformations IIIA and IIIB, the A -strain is relieved if the coplanar
carbonyl group orients towards the axial phenyl group. Equilibrium between the twist
9

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conformations involves pseudo rotation which converts axial hydrogens into equatorial
hydrogens and vice versa, and one of the benzylic hydrogens to occupy the equatorial
orientation. Furthermore, the amide carbon of 3 is expected to be deshielded compared
to parent compound. In the case of N-nitroso-1,4-diazepan-5-one 3 the amide carbon is
shielded by 2 ppm. Hence, the twist-chair conformation is ruled out. In addition, W-
coupling is observed between the amide N-H and H6e with the small coupling constant
value of J=1.6Hz. This suggests that the compound exists in dimeric form holding the NH
in the hydrogen bonded form thus preventing a fast exchange of the N-H and permitting
the NH to couple with C equatorial hydrogen. This is possible only when H , C , C , N
6
6eq
6
5
4
&
4
N -H lie almost in plane, thereby providing a convenient geometric disposition for the
amide lone-pair delocalization. Hence the twist-chair conformation is ruled out.
The twist-boat conformations IVA and IVB require the approximate cis and trans
angles of 30°and 90 °, respectively. However, the observed dihedral angles of 64°& 56°
for 3 eliminate the possibility of twist-boat conformation. Furthermore, the C
3
alkyl
substituents of 3 would be expected to be separated well in the C NMR spectrum. In
contrast, both the signals of these C substituents are found to be very close. Hence the
1
3
3
possibility of twist-boat conformation is also eliminated.
The alternate boat conformation VA and VB requires an approximate cis and trans
dihedral angles of 0-10°and 120-130°. The calcula ted dihedral angles of 64°& 56°of 3
eliminate the possibility of perfect boat conformation.
In the alternate chair conformation IIA and IIB, the α-hydrogens are at equatorial
positions and hence they are in deshielding region of the amide function. The phenyl
1
0

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groups are at axial position and they would exhibit 1,3-diaxial interactions. In order to
3 4
alleviate this strain, the dihedral angle would undergo a change due to twist along C -N
bond. The expected coupling constant value is to be around 2-5 Hz which requires a
dihedral angle to be around 56 °. Thus, the observe d coupling constants and dihedral
angle values of 3 are well accommodated using the alternate chair conformations IIA and
IIB with diaxial phenyl groups.
Hence, it is concluded that the N-nitroso-1,4-diazepan-5-one 3 prefers to exist in an
equilibrium between alternate chair conformations IIA & IIB with diaxial phenyl groups and
the nitroso group adopts coplanar orientation (Figure-7).
3.4 Conformation of N-formyl-c-3,t-3-dimethyl-r-2,c-7-diphenyl-1,4-diazepan-5-one (4)
The possible conformations IA to VA and IB to VB depicted in Figure-6 are also
ruled out for the compound 4 (based on the discussion made for compound 3). The
calculated cis and trans dihedral angles of 4 (both syn & anti rotamers) are 38° & 158°,
respectively.
The calculated dihedral angles conform to the boat forms with flattening at C
3 2
-C -
N -C -C part of the ring. Thus the observed dihedral angle and other observations are
1
1
6
well accommodated by assuming boat conformation with flattening at C
3 2 1 1 6
-C -N -C -C part
of the ring with quasi-equatorial phenyl groups and quasi-axial protons (Figure-8).
The cis dihedral angle between H6e & H7a is found to decrease from 81° to 38°
upon substituting the formyl group at N position. Such a large decrease in dihedral
angles in coplanar orientation leads to the flattening at the C -C -N -C -C part of the ring.
1
The flattening would also result in γ-eclipsing interaction between the C-O and N -C /N -
1
3
2
1
7
6
1
2
1
1

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C
7
7 2
bonds which appears to be responsible for the shielding of C & C α-carbons
compared to parent diazepan-5-one 2.
Thus it is concluded that the N-formyl-1,4-diazepan-5-one 4 prefers to exist in an
equilibrium between flattened boat conformations with coplanar orientation of formyl group
(
Figure-8).
1
3
.5 Dynamic H NMR studies
1
The variable temperature H NMR spectral studies [30] have been carried out for
both the compounds 3 and 4. The doubling of signals of protons is observed at RT due to
syn & anti rotamers of 3 and 4 with the population ratio of 69:31 and 59:41, respectively.
The energy barriers for the N-NO and N-CO rotations are estimated using the modified
Eyring equation derived by Shanon-Aditi and Bar-Eli for the rotamers of unequal
populations [31] (equations 1 & 2).
#
∆
G
AB = 4.57T
c
[10.62+log (X/2Π(1-∆P)+log(T
c
/ ∆ν)cal/mol
(1)
(2)
#
∆
G
c c
BA = 4.57T [10.62+log (X/2Π(1+∆P)+log(T / ∆ν)cal/mol
#
where ∆G is the free energy of activation. T is the coalescence temperature, ∆ν
c
is the chemical shift difference in Hz at T , and ∆P is the population difference between
c
2
3/2
#
#
the rotamers. X value is defined by ∆P = (X -2/3) /X and ∆G AB & ∆G BA are the energy
barriers for the interconversion of rotamer A to B & B to A, respectively.
The changes in shapes of the signals of benzylic protons at C & C of 3 & 4 are
7
2
shown in Figures-9 & 10, respectively. The Tc & ∆ν are found to be 383K and 3.5 Hz for
compound 3 and 388K & 324Hz for compound 4, respectively, and the calculated energy
1
2

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#
#
barriers for the N-NO rotation of 3 are 89.2 (∆G AB) & 88.1 (∆G BA) kJ/mol, with an
#
#
average barrier of 88.7 kJ/mol. Similarly, for N-CO rotation of 4, ∆G AB and ∆G BA are
found to be 76.9 & 74.4 kJ/mol, respectively, with an average barrier of 75.7 kJ/mol.
Furthermore, the energy barrier for 3 is higher than that of 4. It may be due to the greater
polarization of carbonyl group than the nitroso group resulting in an increase in the
repulsion between the charge cloud on oxygen and the Π electrons of the aromatic rings.
Furthermore, N-nitroso-c-3,t-3-dimethyl-r-2,c-7-diphenyl-1,4-diazepan-5-one (88.7kJ/mol )
exhibits a comparable rotational energy barrier with that of the reported N-nitroso-t-3-
isopropyl-r-2,c-7-diphenyl-1,4-diazepan-5-one (89.4kJ/mol) [7].
3.6 Molecular structure determination from crystal data
The crystal structure of the N-nitroso-c-3,t-3-dimethyl-r-2,c-7-diphenyl-1,4-
diazepan-5-one 3 has been investigated by X-ray Crystallographic methods. The ORTEP
plot of the compound 3 is shown in Figure-11. The crystal belongs to the monoclinic
1
space group P2 /c with a= 12.3398(1)Å; b= 20.7988(2)Å; c= 14.0352(1)Å & β=
110.27(2) °. In crystal structure, the asymmetric u nit contains two independent molecules
with almost identical geometry, although they are slightly twisted in opposite directions.
The diazepine ring adopts chair conformation in both the molecules with puckering
parameters [20a] and asymmetry parameters [20b] of q2= 0.3177 (2)Å, q3=0.58 (2)Å, φ2=
-
178.3 (3)°, φ3= -2.11 (2)°& QT= 0.6613 (2)°& q2= 0.3114 (2)Å, q3= 0.5712 (2)Å, φ2= -
74.12 (4) °, φ3= -3.20 (2)° & QT= 0.6505 (2)°, respectively (Figu re-12). The solid state
1
structure of the compound 3 also supports the alternate chair conformation with diaxial
phenyl groups (Figure-12). The molecular structure of the compound 3 and displacement
1
3

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ellipsoid plots drawn at 30% probability level are shown in Figure-13. The crystal data of
the compound 3 are given in Table-5.
2
The N atom of the diazepine ring shows the sp hybridization (360 °) . The nitroso
‘O’ atom is syn to both phenyl rings at C2 & C7 [C2-N1-N2-O2=] 178.58(17); [C7-N1-N2-
O2=] -1.2(3), respectively. In nitroso group, the oxygen atom ‘O’ is disordered with two
positions in one molecule and the occupancies are 0.696 (5)° & 0.304 (5) °. Both the
phenyl rings are substituted at 2,7-positions of the diazepine ring and defined with the
torsion angles [C14-C2-C3-C4=] 65.6(2) ° & [C21-C6- C7-C8=] 55.49(19) °, respectively.
The dihedral angles between the best plane through the diazepine ring and the phenyl
rings are 71.44(19) °& 65.71(19) °. The two pheny l rings are oriented to each other with
a dihedral angle of 25.5 (1) °. The methyl groups [C20 & C21] are oriented axially and
equatorially with respect to the N1 atom, which can be seen from the torsion angle values
of [C20-C6- C7-N1=] -56.49(18) °& [C21-C6-C7-N1=] -174.00(14) °.
The crystal packing is controlled by N—H···O, C-H…N and C—H···O types of intra
and intermolecular interactions in addition to van der Waals forces. The molecules at
(
x,y,z) and (-1-x,1-y,1-z) are linked through intermolecular N5-H5...O1 hydrogen bonds
2
2
into cyclic centrosymmetric R (8) dimers as shown in Figure-13 [32].
3.7. Antibacterial activity
The compounds 2-4 were screened for their in-vitro growth inhibitory action against
different strains of bacteria viz., Staphylococcus aureus, E.coli, Klebsiella pneumonia
using Muller-Hint agar medium by disc diffusion technique. Sterile Muller-Hinton agar
plates were prepared and the agar surface was inoculated with the bacteria: Compounds
2-4 were dissolved in 1mL of DMSO in various concentrations in separate tubes.
Commercially available sterile discs were soaked in the preparation for half an hour. It
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was then placed in empty petri plates for air-drying. Using sterile forceps, the discs were
placed on the surface of the agar plates and gently pressed on to the agar surface. The
°
culture plates were inverted and incubated for 24-48 hrs at 37 C. After incubation, zone of
clearance was observed and its diameter measured using microscope. Zone of inhibition
of extracts were compared with standard chloramphenicol for antibacterial activity. The
results show that the synthesized compounds possess a broad spectrum of activity
against the tested microorganisms and show relatively better activity against all the three
bacterial strains. The results are given in the Table-6.
The parent hexadiazepan-5-one 2 shows a superior antibacterial activity against
Staphylococcus aureus and E.coli and better activity against Klebsiella pneumonia. The
nitroso derivative of hexadiazepan-5-one 3 shows superior activity against E.coli and
Klebsiella pneumonia, good activity against Staphylococcus aureus, and less activity
1
against Salmonella paratyphi. Because of the introduction of formyl group at N position
of compound 4 there is enhanced activity against E.coli and superior activity against
Staphylococcus aureus and Klebsiella pneumonia. The compounds 2 & 4 are inactive
against Salmonella paratyphi. The graphical representation of the antibacterial activity is
presented in Figure 14.
3.8 Antifungal activity
The compounds 2-4 were screened for their antifungal strains viz, Aspergillus niger,
Aspergillus fumigates, and Aspergillus flavus. For antifungal, assays measuring inhibition
of mycelia growth on agar media were used. Compounds 2-4 were dissolved in 1 ml of
sterile Dimethyl sulfoxide (DMSO) serving as a stock solution. Then it was transferred to
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4
ml Sabouraud dextrose agar (SDA) growth media in separate tubes and autoclaved at
21 °C for 15 minutes. These tubes were allowed to cool to 50 C and non solidified SDA
1
of each tube was loaded with various concentration of drug solution. Then the tube was
inoculated with 4 mm diameter piece of inoculums removed from 7 days old culture of
fungus. All these tubes were incubated at 28±1 °C f or 10 days. A relative humidity was
maintained at 40-50% in the incubation room. Growth in the media was determined by
measuring linear growth (mm) of the compounds 2-4, and compared with chloramphenicol
which was used as a standard reference. The results are given in the Table-7.
The hexadiazepan-5-one 2 exhibits superior antifungal activity against Aspergillus
niger & Aspergillus flavus and better activity against Aspergillus fumigates. The nitroso
derivative of hexadiazepan-5-one 3 shows superior activity against Aspergillus niger,
Aspergillus flavus and Aspergillus fumigates. Because of the introduction of formyl group
at N position of compound 4 there is superior activity against Aspergillus flavus and
1
Aspergillus fumigates and better activity against Aspergillus niger. The graphical
representation of the antifungal activity is presented in Figure 15.
Conclusion
Two new compounds viz., N-nitroso and N-formyl-1,4-diazepan-5-ones 3-4 have
been synthesized and characterised by using IR, 1D & 2D NMR spectra and mass
spectra. The compound 3 prefers to adopt an alternate chair conformation with diaxial
phenyl groups and the compound 4 exists in a flattened boat conformation with coplanar
1
orientation of N-X=Y functions. The dynamic H NMR studies have been carried out for
both the compounds and the energy barriers for N-NO and N-CHO rotations are found to
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be 88.7 and 75.7 kJ/mol, respectively. Furthermore, the X-ray crystal structure of
compound 3 also supports the solution state conformation. The antimicrobial activities
have been carried out for the compounds 2-4 and all the compounds exhibit significant
antibacterial and antifungal activities when compared to the standard chloramphenicol.
Additional information
Crystallographic data (CIF and FCF) for the structures of compound (3) reported in
this paper have been deposited with the Cambridge Crystallographic Data Centre as
supplementary publication number, CCDC 1053268. Copies of the data can be obtained
free of charge, on application to CCDC, 12 Union Road, Cambridge CB2 1 EZ, UK. (fax:
+
44-(0)1223-336033 or email: deposit@ccdc.cam.ac.uk).
Acknowledgements
SP thanks UGC for financial assistance in the form of Major Research Project. [No. F.
39-724/2010 (SR)]. We thank (SIF) IISC Bangaluru and (SAIF) IIT Chennai for recording
NMR and Mass spectra.
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Scheme caption:
Scheme 1:
Synthesis of N-nitroso- and N-formyl-1,4-diazepan-5-ones 3 & 4
2
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Figure captions:
Figure-1
Designation of syn and anti rotamers
Figure – 2
1
H NMR spectrum of the compound 4
Figure – 3
13
C NMR spectrum of the compound 4
Figure – 4
HSQC NMR spectrum of the compound 4
Figure-5
Preferred conformation of the compound 2
Figure-6
Possible conformations of N-nitroso- and N-formyl-1,4-diazepan-5-ones 3 & 4
Figure-7
Conformational equilibrium of N-nitroso-1,4-diazepan-5-one 3
2
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Figure-8
Conformational equilibrium of N-formyl-1,4-diazepan-5-one 4
Figure-9
Variable temperature NMR spectra for the compound 3
Figure-10
Variable temperature NMR spectra for the compound 4
Figure-11
ORTEP plot diagram of the compound 3
Figure-12
Solid state diagram of the compound 3
Figure-13
The molecular structure of the compound 3 and displacement ellipsoids is drawn at the
30% probability level.
2
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Figure-14
Graphical representation of antibacterial activities for the compounds 2-4.
Figure-15
Graphical representation of antifungal activities for the compounds 2-4.
2
4

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Table captions
Table 1
Analytical data for the compounds 3 & 4
Table 2
1
H NMR Chemical shift values (δ ppm) of N-nitroso and N-formyl derivatives of c-3,t-3-
dimethyl-r-2,c-7-diphenyl-1,4-diazepan-5-one 3 & 4 compared with parent diazepan-5-one
2
Table 3
13
C NMR Chemical shift values (δ ppm) of N-nitroso and N-formyl derivatives of c-3,t-3-
dimethyl-r-2,c-7-diphenyl-1,4-diazepan-5-one 3 & 4compared with parent diazepan-5-one
2
Table 4
Vicinal coupling constant for the N-nitroso and N-formyl derivatives of c-3,t-3-dimethyl-r-
2,c-7-diphenyl-1,4-diazepan-5-one 3 & 4 compared with parent diazepan-5-one 2
Table 5
Selected bond lengths [Å] for the compound 3
2
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Table 6
Antibacterial activities of the compounds 2-4.
Table 7
Antifungal activities of the compounds 2-4.
2
6

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Table 1
Elemental analysis
Found (Calcd) %
H
Compounds Molecular formula Melting point
Yield
(%)
(
Mol.Wt.)
( °C )
C
N
7
0.46
6.61
(6.50)
13.07
(13.00)
C H N O
1
9
21
3
2
196-198
70
3
4
(70.59)
(
323)
7
4.65
6.67
(6.83)
8.58
(8.70)
C H N O
2
0
22
2
2
220-222
40
(74.53)
(
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Table - 2
cpd
H2
H6ax
H6e
H7a
NH
CH3
‘CH3
Aromatic
protons
CHO
syn Anti syn Anti syn Anti syn Anti N H N H syn Anti syn Anti
syn Anti
4
1
2
3
4
3.87
3.09
2.56
4.03
6.21 1.88
0.88
1.53
7.17-7.36
-
-
5.99 6.53 3.49 2.98 3.62 3.34 6.43 6.63 1.73
5.90 4.41 3.44 3.26 3.23 3.37 5.05 6.25 6.39
1.43 1.58 1.28 1.41 6.70-7.27
-
1.31 1.26 1.62 1.64 6.83-7.18 8.64 8.51