Synthesis, Characterization, and Structural Investigations of 1-(3-morpholinopropyl)-3-(4-chlorobenzoyl)thiourea monohydrate and 1-(3-morpholinopropyl)-3-(4-methylbenzoyl)thiourea monohydrate

Mol. Cryst. Liq. Cryst., Vol. 616: pp. 151–175, 2015

ISSN: 1542-1406 print/1563-5287 online

DOI: 10.1080/15421406.2014.990786

Synthesis, Characterization, and Structural

Investigations of

-(3-morpholinopropyl)-3-(4-chlorobenzoyl)thiourea

monohydrate and 1-(3-morpholinopropyl)-3-(4-

methylbenzoyl)thiourea

1

monohydrate

1

,∗

1

IBRAHIM ABDUL RAZAK, SUHANA ARSHAD,

1

KALIYAPERUMAL THANIGAIMANI, MOHD SUKERI

MOHD YUSOF, SHARIFAH SAKINAH ABDULLAH,

AND AZHAR ABDUL RAHMAN

2

1

School of Physics, Universiti Sains Malaysia, USM, Penang, Malaysia

Faculty of Science and Technology, Department of Chemical Sciences,

2

Universiti Malaysia Terengganu, Mengabang Telipot, Kuala Terengganu,

Malaysia

Two new compounds, 1-(3-morpholinopropyl)-3-(4-chlorobenzoyl)thiourea monohy-

drate (I) and 1-(3-morpholinopropyl)-3-(4-methylbenzoyl)thiourea monohydrate (II)

1

13

have been synthesized and characterized by FT-IR, H NMR, C NMR, and Single-

Crystal X-Ray Diffraction analyses. Theoretical investigations have been calculated by

using DFT method of B3LYP/6-31G + (2d,p) and B3LYP/6-311G + (2d,p) basis sets.

Each compound contains a water molecule, forming intra and intermolecular hydrogen

bonds with other molecules and further stabilizes the crystal structure. Theoretical cal-

culations of bond parameters, harmonic vibration frequencies, and isotropic chemical

shifts are in good agreement with the experimental results. The observed intermolecular

interactions in the crystal packing are the main cause of the calculated torsion angles,

molecular vibrations, and chemical shifts. The calculated molecular vibrations show

good correlation values ranging from 0.995, 0.996, and 0.997 with the experimental

data, where the higher basis set ﬁts the experimental results better.

Keywords Crystal Structure; DFT Studies; Spectroscopy; Thiourea

1. Introduction

Studies on benzoylthiourea derivatives have become one of the interesting subjects due to

its potential as neutral ligands. The sulphur, nitrogen, and oxygen donor atoms provide

a multitude of bonding possibilities [1, 2]. These compounds are able to coordinate the

∗

Address correspondence to Ibrahim Abdul Razak, X-ray Crystallography Unit, School of

Physics, Universiti Sains Malaysia 1800, USM, Penang, Malaysia; E-mail: arazaki@usm.my

Color versions of one or more of the ﬁgures in the article can be found online at

www.tandfonline.com/gmcl.

151

152

I. A. Razak et al.

Figure 1. The ORTEP diagram of compound I with 50% probability displacement ellipsoid.

metal ion where the ligands typically bond as monoanions through S, N, or O [3, 4] atom.

Substituted thiourea derivatives, however, show more diverse coordination chemistry due to

their conformational isomerism, steric effects, and presence of donor sites on the substituent

groups and intramolecular interactions [5–8]. Thiourea derivatives can be regarded as model

compounds for different intra and intermolecular interactions involving S atoms [9, 10]. The

coordination chemistry of substituted thioureas has been applied to many interesting ﬁelds

such as corrosion inhibitor [11–14], agricultural sector [15, 16], pharmaceutical sector [17],

catalyst [18–20], and biological sector [21–25].

In the present, computational studies have been widely used because it helps to simulate

chemical structures and reactions numerically, based in full or in part on the fundamental

law of physics [26]. In order to produce accurate results, choosing the suitable method

and the basis set is indeed an important procedure. Studies [2, 27, 28] have shown that the

use of DFT (Density Functional Theory)/B3LYP (Becke’s three-parameter hybrid method,

Lee, Yang and Parr) method is in a good agreement with the observed data compared to the

HF (Harthree Fock) method. DFT study includes the effect of electron correlation in the

calculation, whereas HF only considers what each electron sees and reacts to an average

electron density [26]. In addition, the use of larger basis sets imposes fewer constraints on

electrons and more accurately approximate exact molecular orbitals [26].

In continuation of our previous studies [29–32], 1-(3-morpholinopropyl)-3-(4-

chlorobenzoyl)thiourea monohydrate and 1-(3-morpholinopropyl)-3-(4-methylbenzoyl)

thiourea monohydrate, namely compound I and compound II, have been synthesized and

1

13

characterized using FTIR, H NMR, and C NMR. In order to study their intra- and in-

termolecular hydrogen bond interactions, the three-dimensional structures of the studied

crystal structures were examined by X-Ray crystallography technique. DFT method of

B3LYP had been employed to optimize the structure of compounds I and II at 6-31G +

(

2d,p) and 6-311G + (2d,p) levels. Herein, we reported the results of geometrical param-

1 13

eters, fundamental frequencies, and GIAO H and C NMR chemical shift for both basis

sets. In combination of the experimental results and quantum chemical calculations, we

would like to explore the effect of intra- and intermolecular hydrogen bonds of I and II at

two different basis sets, and to compare predictions made from calculated results with the

experimental data that correlates well to which basis set.

Molecular Structure Analysis of Carbonylthiourea Derivatives

153

Figure 2. The ORTEP diagram of compound II with 50% probability displacement ellipsoid.

2. Results and Discussion

2.1. X-Ray Crystal Structures

The molecular structure of 1-(3-morpholinopropyl)-3-(4-chlorobenzoyl)thiourea monohy-

drate (I) and 1-(3-morpholinopropyl)-3-(4-methylbenzoyl)thiourea monohydrate (II) were

conﬁrmed by the result of a single crystal X-ray structure diffraction study. Fig. 1 and 2

show the ORTEP diagram of the molecular structure with 50% probability displacement

ellipsoids of compounds I and II respectively. Water molecules (O1W) are trapped in

the asymmetric unit of the title compounds, I and II. The compounds had different para-

substituted atoms of the phenyl ring, which were chlorine atom in I and methyl group in

II. The selected bond lengths and angles are listed in Table 1 and the hydrogen bonding

parameters are listed in Table 2.

All bond lengths and angles were in the normal range and comparable to the related

structures [29–32]. The bond lengths of N1 C7 [1.3762(16) Å for compound I and 1.386(2)

Å for compound II], N1 C8 [1.3959(16) Å for compound I and 1.393(2) Å for compound II]

and N2 C8 [1.3246(17) Å for compound I and 1.321(2) Å for compound II] were shorter

than the normal bond length of N C, which was 1.472 Å. Shorter bond length indicated a

partial double bond character along with resonance interactions within the carbonylthiourea

group. The same resonance interaction was observed for S–C bond [normal S C single

bond = 1.82 Å and normal S C double bond = 1.56 Å], where the bond lengths of

S1 C8 for compounds I and II were 1.6755(14) Å and 1.6880(18) Å, respectively.

Both compounds adopted trans-cis conﬁgurations with respect to the position of

4-chlorobenzoyl and 4-propylmorpholine for compound I and 4-methylbenzoyl and 4-

propylmorpholine for compound II relative to the S1 atom across their C8-N1 and C8-N2

bonds, which were comparable to the previously reported structures [33,34]. It was found

that the intramolecular hydrogen bond between the oxygen atom in the C O group and

the hydrogen atom of the thiourea moiety was favored by the formation of a six-membered

ring. In each compound I and II, an intramolecular N2 H1N2 . . . O2 hydrogen bond was

observed with nonbonding distances of N . . . O and the angles of N H . . . O at 2.6257(15)

◦

Å/139.5 (18) and 2.638(2) Å/135(3) , respectively. The dashed line in the ORTEP diagram

presented in Fig. 1 and Fig. 2 shows the intramolecular hydrogen bond of the compound.

The slight differences in bond lengths and angles for both compounds were due to the

154

155

156

I. A. Razak et al.

◦

Table 2. Hydrogen bonding distances (Å) and angles ( ) in compounds I and II

Bond length, (Å)

Angle

Bond

D—H . . . A

◦

D—H

H . . . A

D . . . A

D—H . . . A, ( )

Compound I

N2—H1N2 . . . O2

N1—H1N1 . . . O1W

O1W—H2W1 . . . N3 #1

O1W—H1W1 . . . S1 #2

C4—H4A . . . S1 #2

0.84(2)

0.85(2)

0.96(3)

0.88(3)

0.95

1.929(19)

2.012(19)

1.87(3)

2.57(3)

2.80

2.6257(15)

2.8447(16)

2.8222(16)

3.4393(12)

3.4468(15)

3.4690(16)

3.4828(16)

139.5(18)

168.5(17)

176(2)

172(2)

126

(

a)

(

a)

(

a)

(

a)

C15—H15B . . . O2 #3

0.99

2.49

2.57

169

154

C14—H14A . . . Cg1 #4⁽^a⁾

(b)

Compound II

N2—H1N2 . . . O2

N1—H1N1 . . . O1W

O1W—H1W1 . . . S1 #5

O1W—H2W1 . . . N3 #6

0.81(3)

2.01(3)

2.12(3)

2.57(3)

2.12(4)

2.46(3)

2.76

2.638(2)

2.955(2)

3.3742(16)

2.888(2)

3.050(2)

3.667(2)

135(3)

176(2)

164(3)

171(4)

131(3)

155

0.84(3)

0.83(3)

0.77(4)

0.81(3)

0.98

(

a)

(

a)

(

a)

N2—H1N2 . . . O2 #7

C16—H16B . . . Cg2 #8⁽^a⁾

(b)

a

Symmetry transformations used to generate equivalent atoms: #1 x−1/2, y+1/2, z; #2 −x+1/2,

y+1/2, −z; #3 −x+1, y, −z+1/2; #4 x+1/2, −y−1/2, z+1/2; #5 −x, −y+1, −z; #6 x, y−1, z; #7

x, −y+2, −z+1; #8 −x−1, −y+1, −z+1.

−

b

Cg1 and Cg2 are the centroids of the benzene ring for compound I and II.

different substituents attached to the benzene ring, which contributed to the electron with-

drawing effect. Saeed et al. [35] reported that an intramolecular hydrogen bond between the

thiourea group and the oxygen atom of the amidic group stabilizes the planar six-membered

ring structure. Formation of this (pseudo) ring is important for the molecular conformations

because it prevents free rotation within the central carbonyl thiourea moiety and locks its

atoms in a nearly planar arrangement [36].

The carbonyl thiourea group (—C(O)NHC(S)NH—) was essentially planar for both

compounds I [maximum deviation of 0.0756 (11) Å at atom N1] and II [maximum deviation

of 0.0846 (14) Å at atom O2] where the dihedral angles of O2-C7-N1, N2-C8-S1 and N1-

◦

C8-S1 within the carbonylthiourea group were 122.78(12) , 123.72(10) , and 119.07(10)

◦

for compound I and 122.69(16) , 124.32(13) , and 118.03(13) for compound II. In addi-

◦

tion, the dihedral angles of C7 N1 C8 were 126.53(11) (compound I) and 126.43(15)

◦

(

compound II) and C8 N2 C9 were 123.37(12) (compound I) and 123.62(15) (com-

2

pound II) where these angles show a sp hybridization on the N1 and N2 atoms. The

benzene rings (C1/C2/C3/C4/C5/C6) were essential planar with maximum deviations of

0.010(1) Å at atom C1 and 0.009(2) Å at atom C4, respectively to compound I and com-

pound II. Meanwhile, the morpholine ring (O1/N3/C12/C13/C14/C15) in both compounds

adopted chair conformations [37] with puckering parameters of Q = 0.5799 (14) Å, ꢀ =

◦

1

=

78.46(15) , and ꢁ = 74(5) for compound I and Q = 0.573 (2) Å, ꢀ = 178.61 (19) , and ꢁ

202 (10) for compound II. The same ring conformations were also reported in the related

compounds that consisted of morpholine ring moiety [38–40]. In compound I, the whole

molecule was almost planar except at the terminal chloro-substituted benzene ring where it

Molecular Structure Analysis of Carbonylthiourea Derivatives

157

Figure 3. Hydrogen bonding interactions in Compound I: (a). Interaction with the water solvent; (b).

C—H . . . π interaction; (c). The crystal packing of the compound connected into a three-dimensional

network.

◦

slightly twisted at C6 C7 bond with the C1 C6 C7 N1 torsion angle of −158.31(12) .

In compound II, the methyl-substituted benzene ring (C1/C2/C3/C4/C5/C6/C16) and the 4-

propylmorpholine ring (O1/N3/C9/C10/C11/C12/C13/C14/C15) were twisted away from

the carbonylthiourea moiety ( C(O)NHC(S)NH ) at C6 C7 bond [C1 C6 C7 N1

◦

torsion angle of 145.83(16) ] and C9 C10 bond [C8 N2 C9 C10 torsion angle of

◦

77.8(2) ].

The crystal structure of compounds I and II is shown in the Figs 3 and 4, respec-

tively. Figures 3(a) and 4(a) show the intermolecular hydrogen interactions between the

main molecules with the water molecules. The same intermolecular N1—H1N1 . . . O1W,

O1W—H2W1 . . . N3, and O1W—H1W1 . . . S1 hydrogen bonds (Table 2) were involved

between the molecules and water solvents in both compounds but displayed different types

158

I. A. Razak et al.

Figure 4. Hydrogen bonding interactions in Compound II: (a). Interaction with the water solvent; (b).

C—H . . . π interaction; (c). The crystal packing of the compound connected into a three-dimensional

network.

of crystal packing arrangement. In compound I, the molecules were linked into a cen-

4

trosymmetric dimer and generate R4 (12) ring motif [41]. Meanwhile in compound II,

the intermolecular interaction between water molecules and the sulphur atoms formed

4

R4 (12) ring motifs [41] and further connected into inﬁnite one-dimensional column by

intermolecular O1W—H2W1 . . . N3 hydrogen bonds (Table 2). The molecules in com-

pound I were connected into a three-dimensional network as shown in Fig. 3(c) by

C4—H4A . . . S1 and C15—H15B . . . O2 hydrogen bonds (Table 2) and stabilized by

C—H . . . π interactions, generated by symmetry transformation of x+1/2, −y−1/2, z+1/2

where π (Cg1) was the centroid of the terminal benzene ring (C1/C2/C3/C4/C5/C6),

Fig. 3(b). Different crystal packing was formed by molecules in compound II, which is

shown in Fig. 4(a)–(c). Intermolecular N2—H1N2 . . . O2 hydrogen bonds (Table 2) con-

nected the molecules into a two-dimensional sheet parallel to bc-axis. These intermolecular

Molecular Structure Analysis of Carbonylthiourea Derivatives

159

Figure 5. Optimized structure of Compound I at (a) DFT B3LYP/6-31G+(2d,p); (b) DFT B3LYP/6-

11G+(2d,p).

3

2

N—H . . . O hydrogen bonds further formed R2 (12) graph-set motifs [41]. C—H . . . π

interactions (symmetry code: −x−1, −y+1, −z+1) involving the centroid of the ben-

zene ring (Cg2 = C1/C2/C3/C4/C5/C6) were also observed. The carbonyl thiourea group

(—C(O)NHC(S)NH—) and the nitrogen atom within the morpholine ring played an impor-

tant role in generating supramolecular hydrogen bond with the water molecules. In addition,

the carbonyl thiourea moieties which contained three potential donor atoms (N, O, and S)

became the utility among organic reagents as potential donor ligands for transition metal

ions.

The molecular structures obtained from X-Ray crystallography analysis were per-

formed a full geometry optimization for the purpose of theoretical and experimental data

comparison. The structures were calculated by DFT method with two different basis sets of

B3LYP/6-31G+(2d,p) and B3LYP/6-311G+(2d,p). Fig. 5 and Fig. 6 show the optimized

structures of both compounds and Table 1 lists out the selected bond lengths and angles

of the optimized structures where the calculated bond lengths and angles were in a good

agreement with the experimental results. The calculated bond lengths and angles for basis

set of B3LYP/6-311G+(2d,p) indicated the best agreement with the experimental values in

both compounds.

The optimized structures for basis set of B3LYP/6-31G+ (2d,p) and B3LYP/6-311G+

(

2d,p) for compound I is shown in Fig. 5(a) and (b), respectively. The bond lengths for

N1 C7 [1.38120 and 1.38044 Å], N1 C8 [1.39887 and 1.39854 Å], and N2−C8 [1.33187

and 1.32914 Å] were in a good agreement with the X-ray diffraction results indicating that

160

I. A. Razak et al.

Figure 6. Optimized structure of Compound II at (a) DFT B3LYP/6-31G+(2d,p); (b) DFT B3LYP/6-

11G+(2d,p).

3

the partial double bond character existed within the optimized thiourea moiety. These bond

characters were the results of the intramolecular N H . . . O hydrogen bond that locked

the molecule to form a six-membered ring motif. In addition, the similar trend of C N

bond lengths has been obtained from these species [N2 C8<N1 C7<N1 C8] and this

trend also reproduced by the quantum chemical calculations suggesting intramolecular are

responsible for the observed N C bond lengths values rather than the crystal packing effects

[

7,35,42]. However, compound II showed the same bond length values for N1−C7 [1.38492

and 1.38418 Å], N1 C8 [1.39686 and 1.39623 Å], and N2 C8 [1.33287 and 1.33027 Å]

but the observed simulated bond length of N1 C7 shown in Fig. 6(a) and (b) possessed a

single bond criteria. The different substituent atom attached to the benzene ring may have

affected the criteria of the optimized C–N bond length, where the substituted-methyl group

(compound II) was the electron donating group as compared to the substituted-chlorine

atom (compound I), which was the electron withdrawing group. Various electron-donating

or -withdrawing substituents affected the hydrogen-bonding ability of the thiourea, which

depended on the acidity of the thioureido NH protons that provided additional bonding

site [35].

From Table 1, the nonhydrogen bonding atoms provide a good result with the exper-

imental data compared to the hydrogen-attached atoms; examples in this compound are

N–H and O H bonds. The calculated N H bond lengths in both compounds for both

basis sets showed higher values than the experimental results [0.82 to 0.85 Å], where the

values varied between 1.01763 to 1.02116 Å. The bond angles of the water molecules

(H2W1 O1W H1W1) were slightly different from the experimental results, where the

Molecular Structure Analysis of Carbonylthiourea Derivatives

161

◦

angle differences ranged between 2 to 4 . The differences between the experimental and

theoretical values were due to the environment factor where the theoretical calculations

were performed in gaseous state, whereas the experimental data belonged to the solid

phase.

From the optimized structure of I, the dihedral angle between the carbonyl thiourea

ring made up by the intramolecular N2 H1N2 . . . O2 and the benzene ring is shown by the

◦

torsion angle C1 C6 C7 O2 value of 14.44255 [B3LYP/6-31G+(2d,p)] and 11.57928

[

B3LYP/6-311G+(2d,p)]. The corresponding torsion angle values in II are −12.83230

◦

[

B3LYP/6-31G+(2d,p)] and −12.39004 [B3LYP/6-311G+(2d,p)]. The differences be-

tween this values compared to the corresponding experimental values [Table 1] are due

to the intermolecular C15 H15B . . . O2^#³(compound I) and N2 H1N2 . . . O2 (com-

pound II) interactions affecting the molecular structure and the intramolecular N H . . . O

hydrogen bond interaction [6]. The signiﬁcant difference between the experimental and the-

oretical values can also be seen with the C15 N3 C11 C10 and C8 N2 C9 C10 tor-

sion angles of compound II which are due to O1W H2W1 . . . N3 and N2 H1N2 . . . O2

intermolecular hydrogen bonds (symmetry code in Table 2), respectively.

#7

2.2. Vibrational Analysis

The harmonic vibrational frequencies calculated at DFT level with the diffused and po-

larization functions, B3LYP/6-31+(2d,p) and B3LYP/6-311G+(2d,p) along with the ex-

perimental frequencies, relative intensities and probable assignments are summarized in

Tables 3 and 4. The experimental and calculated FT-IR spectra for both compounds are

shown in Fig. 7. The calculated frequencies were performed for a free molecule in vacuum,

while the experimental frequencies are in the solid state. Comparison of the calculated and

the experimental frequencies revealed the overestimation of the calculated wavenumbers

corresponding to observed results because of the combination of electron correlation ef-

fects and basis set deﬁciencies. Furthermore, the slight disagreement between theory and

experiment could be due to neglect of the anharmonicity in the real system. Therefore, in

order to improve the agreement with the experiment data, it is customary to scale down the

calculated harmonic wavenumbers. In our study, we have used a scaling factor of 0.9613

and the vibrational wavenumbers suited well with experimental data.

The stretching frequencies of O−H bonds of the water molecule can be observed at

−1

3

487.61 and 3467.70 cm in compounds I and II, respectively. Meanwhile, the stretching

−

1

−1

N−H group was clearly observed in the range of 3100 cm to 3400 cm . The calcu-

lated frequencies of B3LYP/6-31G+(2d,p) and B3LYP/6-311G+(2d,p) gave the values

−1

of wavenumbers at 3365.51 (O−H)/3284.28 (N−H) cm and 3365.41 (O−H)/3274.21

−1

(

3

/

N−H) cm in compound I, respectively. Meanwhile, the corresponding values were

−1

373.57 (O-H)/3268.95 (N−H) cm for B3LYP/6-31G+(2d,p) and 3372.51 (O−H)

−1

3262.85 cm (N−H) for compound II. These assignments were due to the formation

of intra- and intermolecular hydrogen bonds formed by the N−H and O−H bonds.

−1

The strong carbonyl bands were clearly observed at 1666.63 and 1663.09 cm in

compounds I and II, respectively. These values were decreasing compared to the vibration

−

1

of carbonyl group (1710 cm ). Meanwhile, the calculated carbonyl frequencies were

−1

1

643.02 cm [B3LYP/6-31G+(2d,p)] and 1634.85 cm [B3LYP/6-311G+(2d,p)] for

−

1

−1

compound I and 1614.77 cm [B3LYP/6-31G+(2d,p)] and 1633.71 cm [B3LYP/6-

3

11G+(2d,p)] for compound II. Perhaps the strong C O stretching bands were related to

the effect of conjugated resonance with the phenyl ring and the formation of intramolecular

N H . . . O hydrogen bond within the molecules.

162

I. A. Razak et al.

Table 3. Comparison of the theoretical and experimental vibrational spectra and proposal

assignment for compound I

−

1

Calculated IR (km mol

)

Experimental

B3LYP 6-31G + (2d,p)

B3LYP 6-311G + (2d,p)

−

cm ¹)

Assignments ⁽^a⁾

(

Unscaled

862.41

3501.00

427.89

3416.50

Scaled

IRint

Unscaled

Scaled

IRint

3

3712.935

85.73

3860.84

3500.90

3434.17

3406.02

3209.27

3203.24

3196.05

3186.60

3091.17

3089.52

3080.19

3070.52

3053.66

3051.60

3040.17

3030.97

3022.57

2984.83

2980.70

2916.24

2904.16

2898.95

1700.66

1648.18

1631.92

1603.66

1600.15

1578.22

1528.71

1507.98

1500.14

1496.98

1491.57

1487.30

1483.07

1436.64

1435.27

1420.00

1413.37

1404.14

1389.20

1370.42

1365.84

1346.01

1340.98

1335.30

1322.75

1320.61

1308.70

1302.25

1286.92

1281.06

1244.27

1233.80

1219.06

1195.22

3711.425

81.14

ν asOH

ν sOH, ν sNH

ν sCH

νasCH

νasCH2

νsCH2

3

487.61

161.84

3365.511 799.43

3295.231 179.51

3284.281 195.86

3365.415 814.08

3301.268 111.85

3274.207 249.22

3

221.51

216.87

207.75

3201.37

098.22

3096.838

3092.377

3083.610

3077.477

2978.319

2977.358

2967.889

2958.612

2942.347

2939.915

2928.629

2917.113

2911.009

2871.634

2867.212

2.86

2.35

0.53

3085.071

3079.275

3072.363

3063.279

2971.542

2969.956

2960.987

2951.691

2935.483

2933.503

2922.515

2913.671

2905.597

2869.317

2865.347

2.74

2.38

0.41

3

034.64

4.61

7.50

3

26.20

44.98

37.64

31.70

35.73

2.42

17.50

13.16

2.51

23.78

45.31

39.26

30.48

29.33

7.37

13.11

11.77

4.43

2

961.22

939.85

3097.22

3087.37

3

077.72

060.80

058.27

046.53

034.55

3028.20

2987.24

982.64

2

876.24

854.63

94.48

22.12

92.00

19.99

νsCH2

2

829.49

778.82

2917.83

2906.69

898.93

2804.910 140.82

2803.382 129.70

2791.769

2786.761

1634.844 173.67

1584.395 16.14

1568.765 110.74

1541.598 197.58 ν CC, ν CN, δOH, δNH

1538.224 249.76 ν CC, ν CN, δOH, δNH

2794.201

2786.741

36.90

34.84

40.47

28.50

2

νsCH2

1

666.63

1709.16

648.39

634.93

1643.016 181.50

1584.597 19.43

1571.658 106.89

1546.857 214.33

1542.704 215.74

1518.912 851.41

ν CO, δNH

δOH, δNH

ν CC, δNH

1

1592.25

1559.04

1528.24

1486.87

1404.02

1609.13

1604.81

1580.06

1525.39

1517.82

505.84

498.02

494.67

488.77

483.61

479.34

437.47

433.52

416.92

416.12

1405.77

1388.31

1373.50

364.59

342.20

340.26

338.35

333.81

320.60

308.82

1517.143 811.71

ρ CN, δNH

ν CC, ρCH, δNH

δCH2

1466.357

1459.080

1447.564

1440.047

1436.826

1431.155

1426.194

1422.090

1381.840

1378.043

1362.085

1361.316

1351.367

1334.582

1320.346

1311.780

1290.257

1288.392

1286.556

1282.192

1269.493

1258.169

1252.353

62.12

17.87

11.32

14.20

8.71

10.17

0.58

0.54

17.93

23.58

12.13

5.29

35.36

57.98

94.83

0.84

11.80

8.40

28.91

5.30

1469.549

1449.621

1442.085

1439.047

1433.846

1429.741

1425.675

1381.042

1379.725

1365.046

1358.673

1349.800

1335.438

78.09

19.68

12.70

8.28

9.60

1.08

1

δCH2

ωCH2

0.33

5.32

29.53

3.53

11.52

30.73

49.81

ρCH, ωCH2, ν CN

ωCH2, ν CN, δNH

1

378.08

360.74

307.68

1317.385 114.30

1312.982

1293.919

1289.084

1283.624

1271.560

1269.502

1258.053

1251.853

1237.116

8.83 ωCH2, ν CN, δNH, ν CS

1

17.51

12.94

3.70

10.62

28.12

17.65

14.02

16.12

ωCH2

tCH2

ν CC,ρCH

ν CC,ρCH, ν CN, δNH

tCH2

tCH2, ωCH2

tCH2

ν CN, δNH, ν CC

tCH2, ωCH2

tCH2

9.15

21.49

13.89

1292.14

1265.92

1212.18

1302.77

1289.97

1243.58

232.94

217.94

1240.048 366.72

1231.483 415.14

1195.453

1185.225

1170.806

1.26

3.22

36.90

1196.117

1186.052

1171.882

1.93

2.26

25.59

1

ρCH

ν CN, δNH

1

175.88

1206.22

1159.539 166.10

1148.965 154.31

Molecular Structure Analysis of Carbonylthiourea Derivatives

163

Table 3. Comparison of the theoretical and experimental vibrational spectra and proposal

assignment for compound I (Continued)

−

1

Calculated IR (km mol

)

Experimental

B3LYP 6-31G+(2d,p)

B3LYP 6-311G+(2d,p)

cm ¹)

−

Unscaled

Scaled

IRint Unscaled

Scaled

IRint

Assignments ⁽^a⁾

(

1

146.96

1193.95 1147.744

43.71 1189.58 1143.543

56.34 1164.27 1119.213

14.83 1151.65 1107.081

12.65 1141.02 1096.863

28.31 1132.49 1088.663

96.57 1130.36 1086.615

4.36 1112.18 1069.139

97.66

29.07

29.58

25.48

42.76

70.33

9.99

ν CN, δNH, tCH2

ν CN, ρCH

ν CN, ρCH, δCH2

ρCH

ν CN, ν CC, ρCH

ν CN, ν CC, ν CO

ωCH2

1

169.42 1124.163

153.92 1109.263

140.49 1096.353

135.62 1091.672

1

115.09

1133.71 1089.835

115.30 1072.138

1

091.63

071.47

052.30

040.93

010.53

1109.26 1066.332

1096.98 1054.527

1093.10 1050.797

1062.88 1021.747

1051.71 1011.009

99.53 1106.86 1064.025 112.34

ν CN, ν CC, ν CCl

ρCH2

ν CC, ν CS, ν CN

ν CC, ν CS

ν CC, ν CO, ν CN

ν CC, ρCH

ν CC, ν CO, ν CN

tCH

14.85 1092.40 1050.124

7.54 1092.02 1049.759

12.86 1059.42 1018.420

15.61 1048.58 1008.000

14.61

4.91

15.42

18.14

1.32

1

043.98 1003.578

2.23 1039.86

999.6174

027.93

016.76

995.51

990.40

927.28

911.92

883.53

988.1491 44.93 1033.20

977.4114 26.42 1012.96

956.9838

952.0715

891.3943

876.6287 35.02

849.3374 18.26

838.1479 31.02

837.3500 12.09

993.2152 45.37

973.7584 29.77

917.96

900.18

880.98

861.71

850.87

1.27

0.27

7.24

997.07

991.87

925.52

912.19

885.16

870.73

870.23

860.75

846.81

808.08

794.30

777.02

762.90

732.14

726.75

697.13

659.22

645.45

637.19

634.85

609.52

545.91

497.74

497.12

491.78

466.95

431.26

419.22

414.06

377.81

362.24

342.27

333.55

309.81

290.52

277.46

269.82

256.11

234.16

218.32

202.09

958.4834

953.4846

889.7024

876.8882 30.41

850.9043 15.52

837.0327 34.83

836.5521 11.40

827.4390

814.0385

776.8073 10.69

763.5606 44.78

746.9493 65.20

0.63

0.21

6.55

tCH

ν CC, ν CO, ν CN, ρCH2

ν CC, ν CN

ρCH2, tCH2

ρCH2, ωCH

ρCH2

8

71.89

71.06

61.54

49.95

828.1984

817.0569

0.82

1.19

0.93

1.01

ωCH

7

88.60

64.76

810.37

795.54

779.0087 11.82

764.7526 43.99

747.4011 67.10

733.0874

709.3240 48.99

ν CC, ν CO, ν CN, ν CS

ν CS, ν CC

777.49

762.60

737.88

ωCH

ρCH2

ωNH

ν CCl,ν CC, ν CS

tOH

ν CC

ωCH2, ωCS

ρCS, ωCH2

1.13

733.3758

703.8062 61.94

1.83

7

09.24

26.21

725.55

98.02

662.93

697.4712

671.0066

637.2746 255.08

616.7124 1.52

611.8290 17.02

610.9734

586.3449

525.5331 32.35

4.29

2.03

698.6248

670.1511

633.7082 246.94

620.4711 1.85

612.5307 16.87

610.2813

585.9316

524.7833 31.81

478.4775

477.8815

472.7481

448.8790

414.5702

402.9962

398.0359

363.1888

348.2213 63.00

329.0242 20.75 ρCC, ρCN, ρCCl, ρCO, ρCS

320.6416

297.8204 10.24

279.2769

266.7223

259.3780 96.58

246.1985

225.0980

209.8710

194.2691

5.73

1.41

6

641.54

636.46

635.57

2.79

1.28

5.64

1.35

5

48.81

609.95

46.69

ν CC, ν CCl

ν CC, ν CO, ν CN

ν CC, ν CO, ν CN, ν CCl

ω CC, ωCN, ωCS, ωCO

ρCC, ρCN, ρCCl, ρCO

tCH

5

4

89.62

77.23

499.56

497.68

480.2270

478.4198

471.9791

450.4363

414.8010

402.5828

400.7179

361.1220

341.5980 60.01

328.1494 21.12

320.8146

297.4358

279.7960

267.7893 20.87

263.4923 78.52

246.4869

224.2425

212.2550

194.0096

4.73

2.97

7.85

2.73

1.31

0.37

0.87

4.40

2.79

5.28

5.85

2.76

1.65

0.48

0.80

4.59

4

90.98

68.57

4

18.64

431.50

418.79

416.85

375.66

355.35

341.36

333.73

309.41

291.06

278.57

274.10

256.41

233.27

220.80

201.82

ρCH2, ρCC

ρCO, ν CN, ν CS, δNH

ρOH

7.59

9.42

5.43

6.83

ρCH2

ωCH2

tCC, tCN

5.08

4.54

tCC, tCN, ω OH

ρCH2

ρCC, ρCCl, ρCS

ρCH2, ρOH

ρCH2, ρCS

0.72

3.78

6.61

0.63

0.80

4.20

6.61

0.22

164

I. A. Razak et al.

Table 3. Comparison of the theoretical and experimental vibrational spectra and proposal

assignment for compound I (Continued)

−

1

Calculated IR (km mol

)

Experimental

B3LYP 6-31G+(2d,p)

B3LYP 6-311G+(2d,p)

cm ¹)

−

Unscaled

Scaled

IRint

Unscaled

Scaled

IRint

Assignments ⁽^a⁾

(

1

8

7

4

3

2

1

75.70

37.97

30.64

29.37

10.89

09.57

9.16

2.89

4.21

8.69

6.41

2.59

4.51

1.48

4.53

168.9004

132.6306

125.5842

124.3634

106.5986

105.3296

85.70951

79.68216

71.33807

46.80570

35.00093

31.32877

23.56146

20.64872

13.96769

8.66

8.22

1.81

0.34

0.08

4.15

0.28

0.52

0.72

1.86

0.15

0.10

0.03

0.04

0.14

175.17

138.37

132.04

129.56

112.47

107.81

85.31

77.27

75.22

48.15

35.51

33.21

24.50

17.07

11.05

168.3909

133.0151

126.9301

124.5460

108.1174

103.6378

82.00850

74.27965

72.30899

46.28660

34.13576

31.92477

23.55185

16.40939

10.62237

8.65

8.09

1.88

0.33

0.61

3.77

0.19

0.60

0.84

1.65

0.11

0.19

0.01

0.03

0.20

Skeletal vibration

a

Vibrational assignment: ν, stretching; δ, scissoring; ω, wagging; ρ, rocking; t, twisting.

−1

The C N vibration bands were observed at 1551, 1265, and 1171 cm , respec-

tively, to δCN H, νC(O) N, and νC(S) N as reported in the related structure of thiourea [33].

−

1

The same vibrational bands of δCN H/νC(O) N/νC(S) N at 1528.24/1265.92/1175.88 cm

−1

and 1554.37/1261.08/1174.80 cm can be clearly seen in compounds I and II, re-

−1

spectively. The wavenumbers of 1528.24 and 1554.37 cm showed the bending vi-

bration of CN H and revealed the existence of intramolecular N H . . . O hydrogen

bond. Meanwhile, the determinations of the other two vibrational bands were by the

help of DFT method calculations, where the stretching C N vibrations were assigned

within the same range with the experimental values. The calculated bending and stretch-

1

ing C N bands appeared at 1518.91/1240.05/1159.54 cm [B3LYP/6-31G+(2d,p)] and

−1

1

517.14/1231.48/1148.97 cm [B3LYP/6-311G+(2d,p)] for compound I, whereas in com-

−1

pound II the values were 1528.31/1240.69/1137.82 cm [B3LYP/6-31G+(2d,p)] and

−1

1

527.24/1232.87/1131.38 cm [B3LYP/6-311G+(2d,p)]. The high value of C N ab-

sorption observed in the experimental and theoretical analysis maybe related to δ(C H)

contribution from the substituent group [5]. The lower vibration frequency of νC N, which

−1

normally is around 1300 cm could be due to the mass effect around the nitrogen atom

43].

The IR absorptions of C S band were observed at 764.76 and 756.76 cm for

[

−1

compounds I and II, respectively and the values were in a good agreement with the

calculated values. The calculated B3LYP/6-31G+(2d,p)/B3LYP/6-311G+(2d,p) showed

−1

the values of 679.47/698.62 cm and 731.62/720.35 cm , respectively. The formation of

the intermolecular hydrogen bond interactions between the water molecule and the sulphur

atoms may have affected the values ν(C S), where the presence of intermolecular hydrogen

bonds were conﬁrmed by the X-Ray analysis.

The frequency values computed at B3LYP/6-31G+(2d,p) and B3LYP/6-311G+(2d,p)

level contained known systematic error. By plotting the calculated values against experi-

mental frequency, linearity between the experimental and calculated vibrational frequency

can be determined, which has been presented in Fig. 8. Different basis sets somehow would

Molecular Structure Analysis of Carbonylthiourea Derivatives

165

Table 4. Comparison of the theoretical and experimental vibrational spectra and proposal

assignment for compound II

−1

Calculated IR (km mol

B3LYP 6-31G+(2d,p) B3LYP 6-311G+(2d,p)

Unscaled Scaled Unscaled Scaled

863.29 3713.7807 85.69 3862.38 3712.9059

3509.38 3373.5670 786.01 3508.28 3372.5096 795.66

440.84 3307.6795 102.15 3440.28 3307.1412 92.67

3400.55 3268.9487 338.59 3394.20 3262.8445 337.55

)

Experimental

(

cm ¹

−

)

IRint

81.20

Assignments⁽^a⁾

νasOH

νsOH, νsNH

ν sNH

3

467.70

436.19

3

214.24 3089.8489

208.77 3084.5906

176.42 3053.4925 12.19 3164.95 3042.4664

172.10 3049.3397 15.10 3161.69 3039.3326

3.03 3202.24 3078.3133

5.06 3195.46 3071.7957

2.86

5.82

νsCH

νasCH

νaCH3

νasCH2

νsCH2

νasCH2

νasCH3

νasCH2

νsCH2

νasCH2

νsCH3

11.05

13.98

12.72

15.83

24.90

44.77

17.30

15.18

16.16

42.02

37.12

10.20

13.05

22.49

93.10

21.63

3

144.83

3114.82 2994.2765 13.70 3104.59 2984.4424

3

111.48 2991.0657 17.30 3101.99 2981.9430

098.77 2978.8476 26.50 3090.78 2971.1668

2

957.67

940.02

3095.97 2976.1560 46.11 3088.11 2968.6001

3093.48 2973.7623 12.97 3084.40 2965.0337

3

084.72 2965.3413 12.86 3076.25 2957.1991

081.30 2962.0537 19.53 3073.38 2954.4402

2

857.98

3056.51 2938.2231 43.45 3050.12 2932.0804

3048.24 2930.2731 40.70 3043.88 2926.0818

3041.44 2923.7363 11.23 3036.16 2918.6606

3033.77 2916.3631 13.77 3029.02 2911.7969

3029.20 2911.9700 27.24 3024.33 2907.2884

2986.28 2870.7110 95.62 2983.73 2868.2596

2981.66 2866.2698 23.59 2979.51 2864.2030

νsCH2

2

1

829.28

777.22

215.73

663.09

608.55

564.17

2918.76 2805.8040 134.37 2916.48 2803.6122 126.07

νsCH2

2908.81 2796.2391 39.66 2907.28 2794.7683

2902.29 2789.9714 29.66 2900.69 2788.4333

38.30

28.73

1707.86 1641.7658 171.49 1699.48 1633.7101 164.81

νCO, ρNH, νCC

νCC, ρNH

δOH, ρNH

νCN, ρNH, νCC

νCN, ρNH, νCC, δOH, νCO

ρ CN, δNH

νCC, ρCH, ρNH

δCH2

1654.13 1590.1152 60.64 1650.48 1586.6064

1646.62 1582.8958 28.02 1645.48 1581.7999

52.53

32.82

1

611.41 1549.0484 204.35 1606.38 1544.2131 106.64

607.98 1545.7512 131.52 1603.18 1541.1369 245.84

1

554.37

530.60

1589.83 1528.3036 851.30 1588.72 1527.2365 815.40

1547.25 1487.3714 30.46 1549.22 1489.2652

41.80

9.95

1.08

12.86

10.30

6.30

1.81

9.37

1.03

3.11

1

509.84 1451.4092

497.53 1439.5756

492.82 1435.0479

9.24 1512.50 1453.9663

1.51 1500.51 1442.4403

5.81 1492.54 1434.7787

δCH2

δCH2, δCH3

δCH2

488.08 1430.4913 10.21 1491.54 1433.8174

486.42 1428.8955

483.44 1426.0309

482.83 1425.4445

477.86 1420.6668

441.43 1385.6467

6.21 1488.54 1430.9335

9.09 1486.88 1429.3377

1.91 1485.68 1428.1842

1.22 1481.67 1424.3294

3.03 1443.92 1388.0403

δCH3

δCH2

νCC, ρCH, δCH3

ωCH2

434.23 1375.8414 17.62 1434.21 1378.7061

15.60

3.54

0.72

417.45 1362.5947

415.08 1360.3164

414.20 1359.4705

2.86 1417.88 1363.0080

1.53 1415.37 1360.5952

0.38 1415.23 1360.4606

ωCH2

ωCH2, ωCH3

ωCH2

1.91

1

403.32

376.48

359.97

309.69

1405.49 1351.0975 17.65 1405.80 1351.3955

1387.70 1333.9960 51.73 1387.32 1333.6307

1379.10 1325.7288 84.80 1375.68 1322.4412

13.54

34.12

84.98

4.47

ωCH2

ρCH, ρNH, νCN, ωCH2

ρCH2

1365.22 1312.3860

6.18 1366.97 1314.0683

1

354.97 1302.5327 19.73 1359.05 1306.4548

20.56

49.10

11.54

66.34

10.39

νCC, ρCH

νCC, ρCH, ωCH2

tCH2

346.21 1294.1117 39.67 1344.27 1292.2468

336.61 1284.8832 33.44 1333.79 1282.1723

310.00 1259.3030 28.58 1311.25 1260.5046

309.02 1258.3609 46.66 1308.31 1257.6784

tCH2

1

261.08

213.71

1290.64 1240.6922 400.63 1282.50 1232.8673 234.19

νCC, νCN, ρCH, ωCH2

tCH2

1261.17 1212.3627 66.47 1260.51 1211.7283

69.09

3.81

1

236.94 1189.0704

0.74 1235.08 1187.2824

4.91 1233.62 1185.8789

νCC, ρCH

ρCH2

νCC, ρCH

233.57 1185.8308

222.56 1175.2469 90.78 1221.41 1174.1414

97.02

92.80

214.06 1167.0759 81.51 1209.98 1163.1538 104.93 νCC, νCN, νCO, ρCH2, ρCH, ρNH

166

I. A. Razak et al.

Table 4. Comparison of the theoretical and experimental vibrational spectra and proposal

assignment for compound II (Continued)

−1

Calculated IR (km mol

B3LYP 6-311G+(2d,p)

IRint Unscaled Scaled

78.35 1176.93 1131.3828 104.93 νCC, νCN, νCO, ρCH2, ρCH, ρNH

)

Experimental

B3LYP 6-31G+(2d,p)

(

cm ¹

−

)

Unscaled

Scaled

1183.63 1137.8235

1171.09 1125.7688

IRint

Assignments⁽^a⁾

1

174.80

146.41

36.24 1165.74 1120.6259

23.53 1151.20 1106.6486

30.58 1150.57 1106.0429

30.39

20.48

39.43

97.08

38.21

28.64

6.92

41.00

10.51

15.67

7.43

νCC, νCN, νCO, ρCH2, ρNH

νCC, νCN, νCO, ρCH2, ρCH

νCC, ρCH

νCC, νCN, νCO, δCH2

νCC, νCN, νCO, ρCH2

νCC, νCN, νCO, ρNH.

ρCH2

νCC, νCN, νCS, ρNH

tCH3

νCC, νCN, νCO, ωCH2

νCC, ρCH2, ρCH3

νCC, νCN, νCO, ωCH2

ωCH3

1

153.23 1108.6000

150.16 1105.6488

1117.69

1079.85

1041.91

1133.86 1089.9796 107.58 1130.20 1086.4613

1123.52 1080.0398

1100.23 1057.6511

092.57 1050.2875

1082.62 1040.7226

065.87 1024.6208

1062.96 1021.8234

26.28 1121.57 1078.1652

23.57 1095.57 1053.1714

7.09 1091.91 1049.6531

36.97 1080.25 1039.4056

9.66 1063.42 1022.2656

10.40 1063.33 1022.1791

5.52 1047.83 1007.2790

1

015.62

004.05

1

049.82 1009.1920

034.70 994.65711 11.01 1039.67 999.43477

013.34 974.12374 24.68 1032.50 992.54225

9.70

7.88

4.96

0.85

008.24 969.22111

96.24 957.68551

987.97 949.73556

0.66 1009.61 970.53809

0.78 996.79 958.21423

1.32 988.58 950.32195

9

tCH

968.95

916.47

881.43

861.68

841.74

810.03

1.01

925.60 889.77928 12.73 924.77 888.98140 11.84

905.96 870.89935 13.85 906.45 871.37039 11.02

882.88 848.71254 42.80 882.41 848.26073 41.85

νCC, νCN, νCO, ωCH2

νCC, νCN, νCO

νCC, νCN, νCO, tCH2

νCC, νCN, νCO, ρCH2

ωCH, ωNH, tCH3

νCC, νCN, νCS

νCC, νCN, νCO, ωNH

ωNH

867.47 833.89891

860.47 827.16981

6.21 867.98 834.38917

2.82 860.34 827.04484

9.61 856.05 822.92087

2.26 820.19 788.44865

5.08 800.35 769.37646

5.10 795.03 764.26234

7.07

5.14

9.30

2.39

3.84

7.30

8

7

59.04 825.79515

19.04 787.34315

04.08 772.96210

99.59 768.64587

794.59

756.76

714.17

775.07 745.07479 118.09 771.58 741.71985 118.10

761.07 731.61659 15.37 762.28 732.77976 14.91

754.91 725.69498 23.46 751.58 722.49385 19.34

ωNH

νCS, ρCH2

ωNH

7

49.40 720.39822 17.87 749.35 720.35016 27.65

705.03 677.74534 3.33 703.19 675.97655 3.38

664.81 639.08185 232.11 660.88 635.30394 221.83

νCS, νCC, ρCH2

νCC, ωNH

684.66

629.19

618.68

ωOH

650.36 625.19107

0.50 654.68 629.34388

1.73

νCC

642.30 617.44299 14.68 643.30 618.40429 17.68

ωCS, ωNH

632.65 608.16645

4.12 633.69 609.16620

4.50

ρCH2

5

91.01

617.78 593.87191 28.16 618.24 594.31411 28.22

νCC, νCS, ρCH2

νCC, ωCS, ρCH2

νCC, ωCS, ωCH2

νCC, νCO, νCN, ωCH2

νCC, νCO, νCN

tCC,νCC, νCO, νCN

νCC, νCO, νCN

tCC,

ρCO, ρCC

ρOH

ρCH2

ρCH2, ρCH3

tOH

ρCN, ρCC

ρCH2

ρCN, ρCS

ρCC, ρCS, ρOH

ρCH2

Skeletal vibration

5

4

82.45 559.90919

23.37 503.11558

01.48 482.07272

94.70 475.55511

2.02 582.12 559.59196

6.43 522.98 502.74067

1.10 500.91 481.52478

0.81 495.55 476.37222

5.15 482.95 464.25984

3.96 449.09 431.71022

0.37 421.10 404.80343

0.06 415.20 399.13176

9.91 388.81 373.76305

1.87

6.10

0.85

0.68

5.67

4.01

0.44

0.16

9.89

476.73

49.76

485.70 466.90341

448.62 431.25841

4

3

2

1

21.37 405.06298

15.38 399.30479

87.01 372.03271

57.16 343.33791 15.26 358.76 344.87599 26.40

47.91 334.44588 56.94 355.46 341.70370 44.96

36.91 323.87158 10.10 336.37 323.35248

9.80

7.68

9.84

4.10

28.68 315.96008

08.95 296.99364

88.68 277.50808

7.62 328.30 315.59479

9.42 308.84 296.88789

4.11 286.30 275.22019

77.30 266.56849 97.85 276.25 265.55913 99.88

62.23 252.08170

56.31 246.39080

54.11 244.27594

08.27 200.20995

66.13 159.70077

62.29 156.00938

54.53 148.54969

29.56 124.54603

3.03 262.11 251.96634

0.37 256.53 246.60229

7.27 254.92 245.05460

1.35 207.81 199.76775

1.81 168.22 161.70989

8.38 163.13 156.81687

3.90 152.67 146.76167

4.77 131.76 126.66089

2.97

0.25

7.82

1.57

2.87

6.65

3.76

5.34

Molecular Structure Analysis of Carbonylthiourea Derivatives

167

Table 4. Comparison of the theoretical and experimental vibrational spectra and proposal

assignment for compound II (Continued)

−1

Calculated IR (km mol

)

Experimental

B3LYP 6-31G+(2d,p)

B3LYP 6-311G+(2d,p)

(

cm ¹

−

)

Unscaled

Scaled

IRint

2.00

0.52

0.76

1.26

0.56

2.33

0.08

0.32

Unscaled

Scaled

IRint

0.90

1.57

0.71

1.15

0.58

2.45

0.13

0.20

Assignments⁽^a⁾

Skeletal vibration

ρCH3

1

8

6

5

1

15.57

11.18

04.39

111.09744

106.87733

100.35011

84.219493

61.571265

50.718188

18.524251

14.448339

114.82

111.57

102.78

88.35

64.19

51.79

25.28

14.96

110.37647

107.25224

98.802414

84.930855

61.705847

49.785727

24.301664

14.381048

7.61

4.05

2.76

9.27

5.03

Skeletal vibration

^aVibrational assignment: ν, stretching; δ, scissoring; ω, wagging; ρ, rocking; t, twisting.

Figure 7. The IR spectrum of Compound I: (a) Experimental; (b) B3LYP/6-31G +(2d,p);

c) B3LYP/6-311G +(2d,p) and Compound II: (d) Experimental; (e) B3LYP/6-31G+(2d,p); (f)

B3LYP/6-311G +(2d,p).

(

168

I. A. Razak et al.

Figure 8. The linear corrected between the calculation and FT-IR spectrum of compound I and II.

provide different values of correlation coefﬁcient, where a good linearity between the cal-

culated and experimental frequencies were obtained from higher basis sets. As can be seen

from the correlation graphic [Fig. 8], obtained correlations were 0.996 and 0.997 for com-

pound I and 0.995 for compound II. The use of higher extended basis set has correlated

the experimental and theoretical data well.

2.3. NMR Analysis

1

13

1

Both compounds were characterized by using H and C NMR. The H 400.11 MHz and

13

C 100.61 MHz NMR spectra were recorded in solvent of CDCl3 at room temperature

by Bruker Avance III 400 Spectrometer. Theoretically, the compounds were calculated by

using DFT method with basis sets of B3LYP/6-31G+(2d,p) and B3LYP/6-311G+(2d,p).

The results of the calculated values shifted to higher values of chemical shift and further

corrected with the TMS isotropic chemical shift values. All the experimental and calculated

results are tabulated in Table 5. As can be seen from the table, the experimental and

theoretical values were in a good agreement where the values had the same range of

chemical shift.

1

In H NMR, the NH resonance can be clearly seen where two single peaks were

observed at the most downﬁeld area (10.867 and 8.977 ppm in compound I and 10.947

and 9.010 ppm in compound II). Meanwhile, the calculated chemical shifts showed higher

values for about 1 to 2 ppm differences but the use of basis set B3LYP/6-311G+(2d,p) gave

a better agreement with the experimental results. The high shifted values were due to the

presence of strong intra and intermolecular N—H . . . O hydrogen bonds in the molecules.

The hydrogen atoms of the aromatic ring, morpholine ring, and the methylene group were

generally in the same range as the previously reported studies [3,9,33,36]. These results

were also conﬁrmed by the calculated values, where the values did not deviate higher than

the experimental results (Table 5). The presence of the methyl group in compound II gave

single peaks at δ values of 2.455 ppm and the values of the calculated chemical shift of

methyl group were also in same range of 2.0856–2.7125 ppm for B3LYP/6-31G+(2d,p)

Molecular Structure Analysis of Carbonylthiourea Derivatives

169

Table 5. The experimental and calculated NMR chemical shift of compounds I and II

Compound I

Compound II

Chemical

B3LYP

6-311G +

(2d,p)^c

B3LYP

6-311G +

(2d,p)^c

Shift, δ

6-31G +

ppm)^a

Experimental

(2d,p)

b

Experimental

(2d,p)

b

(

¹H NMR

N1–H1N1

N2–H1N2

Aromatic

Proton

10.867

8.977

7.816, 7.518

11.3438

11.2097

8.7768,

8.3515,

11.0203

10.9460

8.9947,

8.5393,

7.7711,

7.6654.

3.8083,

3.7728,

3.7501,

3.7220,

2.7800,

2.4526,

2.4157,

2.0030.

3.5353,

3.3432,

2.5210,

2.2601,

2.0410,

1.8194.

10.947

9.010

7.758, 7.328

11.2099

11.7561

8.6511,

8.5817,

7.4506,

7.3907

3.7220,

3.6799,

3.6253,

3.5612,

2.6621,

2.3000,

2.2626,

1.9335.

4.1952,

2.9423,

2.3863,

2.1838,

2.1082,

1.3327.

2.7125,

11.0196

11.4272

8.6804,

8.5982,

7.5257,

7.4027.

3.7225,

3.6723,

3.6226,

3.5330,

2.7090,

2.4193,

2.3713,

2.0912.

4.1442,

2.9224,

2.4193,

2.3625,

2.2082,

2.1677.

2.7475,

2.3868,

2.1680.

7

.6150,

.5960.

Proton of

Morpholine

moiety

3.775, 2.494,

3.7561,

3.7247,

3.6701,

3.771, 2.488

3.6114,

2.6598,

2.3614,

2.2896,

1.9317.

Methylene

3.827, 1.916,

3.4277,

3.3609,

3.823, 1.916,

1.765

1.710

2.3538,

2.1948,

2.0308,

1.7763.

Methyl group

2.455

2.4085,

.0856.

2

¹³C NMR

C8

C9

C3

C6

179.39

165.30

140.12

130.23

129.50

179.503

164.159

145.292

127.265

129.309,

189.981

171.521

154.291

134.735

136.519,

133.689

133.154,

132.515

70.307,

70.1251

58.573,

54.7693

60.1520

47.0636

29.3706

179.72

166.40

144.53

129.81

128.95

179.382

163.744

140.674

126.806

127.614,

125.277

126.577,

126.431

69.0633,

68.8558

57.6925,

52.8373

58.1384

45.1407

29.7854

25.5784

191.037

172.188

150.231

133.494

135.879,

132.694

133.165,

132.319

70.2985,

70.1022

58.6170,

54.735

C1 & C5

1

26.611

126.133,

25.561

68.8281,

8.4852

57.7378,

4.0620

C2 & C4

128.84

66.79

53.85

127.47

66.81

53.82

1

C14 & C13

C15 & C12

6

5

C11

C9

C10

C16

56.76

44.94

24.60

58.6090

46.7859

30.3144

56.69

44.72

24.72

21.65

59.4288

45.0386

29.6148

22.6210

^aThe atoms numbering are referred to the X-ray molecular diagram in Fig. 1.

b

The isotropic chemical shift with respect to Tetramethysilane (TMS) in B3LYP 6-31G + (2d,p)

1

13

are 31.6143 ppm for H NMR and 191.2113 ppm for C NMR.

b

The isotropic chemical shift with respect to Tetramethysilane (TMS) in B3LYP 6-311G + (2d,p)

1

13

are 31.8821 ppm for H NMR and 182.4656 ppm for C NMR.

170

I. A. Razak et al.

and 2.7475–2.1680 ppm for B3LYP/6-311G+(2d,p). In addition, the different substituent

atom or group did not affect the values of the chemical shift.

13

In CNMR, the highest δ values were from the thione (C = S) and carbonyl groups

C = O). These groups were at the most deshielded area compared to other carbon atoms

(

because of the environmental factor and the increase of electronegativity from sulphur and

oxygen atoms. Aydin et al. [9] in their report stated that the carbon atoms of thiocarbonyl

∗

showed that the highest value (180.41 ppm) was due to the lower excitation energy n–π and

the possibility of a very strong electron-withdrawing neighbors reduced the nucleophilic

character of the thione group. From Table 5, δ values of thione group and carbonyl group

were 179.39 (δC S) and 165.30 (δC O) ppm (compound I) and 179.72 (δC = S) and 166.40

(

δC = O) ppm (compound II), whereas theoretical values gave higher values of C = S and C =

O chemical shift from B3LYP/6-311G+(2d,p) basis set where the difference was almost 10

to 11 ppm. Meanwhile, the B3LYP/6-31G+(2d,p) showed a very good agreement with the

experimental values. Other carbon atoms were located in the same range as the previously

reported structures [3,9,33,36] and calculated δ values were in a good agreement with the

experimental results especially from the B3LYP 6-31G+(2d,p) basis set.

1

13

As seen from Table 5, the results of the H and C NMR calculated from two different

basis sets were not systematic in relation with the experimental results and it was difﬁcult

to decide which basis sets showed the best agreement with the experimental values. Even

though in the same basis set, there were some values in a very good agreement and there

were some that showed big differences with experimental values.

3. Experimental

3.1. Physical Measurement

Infrared spectra of the compounds were recorded from KBr discs in the spectral range

−

1

of 400–4000 cm by using FTIR Pelkin-Elmer System 100 Spectrometer. The H NMR

(

1

3

400.11 MHz) and C NMR (100.61 MHz) spectra were recorded on Bruker Avance III 400

Spectrometer in solution of deuterated chloroform (CDCl3) as solvents at room temperature

in the range of 0–15 ppm and 0–200 ppm. The chemical shifts were also referenced to the

trimethylsilyl (TMS) as internal standard.

3.2. Synthesis

The reaction process of compounds I and II is shown in Scheme 1. The reactions were

done under ambient temperature. All the chemicals used were purchased from suppliers

and used without further puriﬁcations.

3.2.1. Compound I. A solution of 4-chlorobenzoyl chloride (1.0 g, 6 mmol) was added

dropwise to ammonium thiocyanate in acetone (50 ml). The resulting solution was reﬂuxed

with constant stirring for 1 h. The product was cooled down at room temperature and

3-morpholinopropyl amine (1.0 g, 6 mmol) in 50 ml acetone was added dropwise. The

solution mixture was reﬂuxed with stirring for 4 h. The solution was ﬁltered and the

solution was poured into ice. The solid product was recrystallized to obtain yellow crystal

−1

product (1.21g, 59%). FT-IR (KBr, cm ): 3487.61 (νOH), 3161.84 (νNH), 2961.22, 2939.85,

854.63, 2829.49 (νCH, νCH2), 1666.63 (νC=O), 1528.24, 1265.92, 1175.88 (νCN), 764.76

2

1

(

νC=S). H NMR (CDCl3; δ, ppm): 10.867, 8.977 (2 × s, 1H, NH), 7.816 (d, J = 3.4 Hz,

2

H, Ar), 7.518 (d, J = 2.4 Hz, 2H, Ar), 3.775 (t, J = 4.8 Hz, 4H, proton of morpholine

Molecular Structure Analysis of Carbonylthiourea Derivatives

171

Scheme 1. The reaction process for compound I and II.

ring), 2.494 (t, J = 6.6 Hz, 4H, proton of morpholine ring), 3.827 (q, J = 18.8 Hz, 2H,

13

CH2), 1.916 (t, J = 6.8 Hz, 2H, CH2), 1.710 (m, 2H, CH2). C NMR (CDCl3; δ, ppm):

1

79.39 (C = S), 165.30 (C = O), 140.12, 130.23, 129.50, 128.84 (aromatic ring), 66.79,

53.85 (morpholine ring), 56.85, 44.94, 24.60 (methylene).

3.2.2. Compound II. Compound II was synthesized with a similar procedure as described

in compound I but solution of 4-methylbenzoyl chloride (1.0 g, 6 mmol) was used. Colour-

−1

less crystals were obtained (1.19 g, 62%). FT-IR (KBr, cm ): 3467.70 (νOH), 3436.19,

3

1

4

3

2

1

144.83 (νNH), 2957.67, 2940.02, 2857.98, 2829.28 (νCH, νCH2), 1663.09 (νC O), 1554.37,

1

261.08, 1174.80 (νCN), 756.76 (νC S). H NMR (CDCl3; δ, ppm): 10.947, 9.010 (2 × s,

H, NH), 7.758 (d, J 8.4 Hz, 2H, Ar), 7.328 (d, J = 8 Hz, 2H, Ar), 3.771 (t, J = 4.8 Hz,

H, proton of morpholine ring), 2.488 (t, J = 6.4 Hz, 4H, proton of morpholine ring),

.823 (q, J = 18 Hz, 2H, CH2), 1.916 (t, J = 6.8 Hz, 2H, CH2), 1.765 (m, 2H, CH2),

.455 (s, 3H, methyl). ¹³C NMR (CDCl3; δ, ppm): 179.72 (C S), 166.40 (C O), 144.53,

29.81, 128.95, 127.47 (aromatic ring), 66.81, 53.82 (morpholine ring), 56.69, 44.72, 24.72

(methylene), 21.65 (methyl).

172

I. A. Razak et al.

Table 6. Crystallographic data for compound I and II

Compound

I

II

CCDC deposition numbers

Molecular formula

Molecular weight

Crystal system

Space group

a/Å

944766

C15H20ClN3O2S.H2O

359.87

Monoclinic

C2/c

16.4318

13.0017

16.2908

90.000

97.394

944767

C16H23N3O2S.H2O

339.45

Triclinic

P-1

9.3319(3)

9.6187(3)

10.3072(3)

112.734(1)

90.143(2)

93.455(2)

851.42(5)

2

b/Å

c/Å

◦

α /

β/

γ /

90.000

3451.45(5)

8

3

V/ Å

Z

−

3

Dcalc (g cm )

1.385

1.324

Crystal Dimensions (mm)

μ/mm

₀0_..₃3₆5 × 0.29 × 0.19

₀0_..₂2₁8 × 0.17 × 0.15

−1

Radiation λ (Å)

Tmin/Tmax

Reﬂections measured

Ranges/indices (h, k, l)

0.71073

0.884/0.936

26263

0.71073

0.944/0.969

4887

23 ≤ h ≤ 22;

13 ≤ h ≤ 13;

13 ≤ k ≤ 12;

24 ≤ l ≤ 14.

2.1–30.0

4887

1

2

8 ≤ k ≤ 18;

3 ≤ l ≤ 18.

2.0–30.2

5105

◦

θ limit ( )

Unique reﬂections

Observed reﬂections (I > 2σ(I))

Parameters

4342

218

4031

226

Goodness of ﬁt on F²

R1, wR2 [I ≥ 2σ(I)]

1.04

1.06

0.040, 0.096

0.60 and -0.58

0.047, 0.134

0.45 and -0.29

−

3

Largest diff. peak and hole, e/Å

3.3. X-Ray Crystallography Studies

The single crystal of compounds I and II was mounted on the glass ﬁber. The crystal

structures were determined by single crystal X-ray diffraction from data collected at low

temperature (100K) using the Oxford Cryosystem Cobra low-temperature attachment [45].

The data were collected using a Bruker APEX2 CCD diffractometer with the graphite

monochromated MoKα (λ = 0.71073 Å) radiation and with APEX2 software [46]. The

collected data were reduced using SAINT program [46]. The empirical absorption correc-

tions were performed by the SADABS program [46]. The structure was solved by direct

methods and reﬁned by full matrix least-squares using the SHELXTL software package

[47]. The nonhydrogen atoms were reﬁned anisotropically. The hydrogen atoms which

bounded to the nitrogen atom and the oxygen of the water molecule were found from the

difference fourier maps and reﬁned freely. All the other hydrogen atoms were positioned

Molecular Structure Analysis of Carbonylthiourea Derivatives

173

geometrically and reﬁned using riding model. A rotating group model was applied to the

methyl group of compound II. Besides, the studied structure of compound II was an inver-

sion twin with a domain ratio of 0.81387 (22): 0.18613 (22). In the ﬁnal reﬁnement, the

ij

same U parameter (EADP constraint) was used to the atom pair S1 and C8 of compound

I and ten outliers (−1 −1 2, 7 −2 4, 8 0 1, 5 0 1, −4 0 1, −1 0 1, −5 −2 4, 0 0 1, −1 −2 4,

and 6 −2 4) were omitted from compound II. The structure analysis and presentation of the

results were made using PLATON [47]. Table 6 shows the main crystal data and structure

reﬁnement for compounds I and II.

3.4. Computational Calculation

The molecular geometries were optimized to standard convergence criteria and harmonic

frequencies calculated by using DFT hybrid method with Becke’s nonlocal three parameter

exchange and the Lee, Young and Parr correction (B3LYP) using the 6-31G+(2d,p) and 6-

3

11G+(2d,p) basis sets as implemented in the GAUSSIAN 09 program package [49]. The

optimized structural parameters were used to calculate the vibrational wavenumbers and

isotropic chemical shifts. The calculated vibrational frequencies corresponded to potential

energy minima in which no imaginary frequency was found. The gauge-invariant atomic

orbital (GIAO) method was used to calculate the H and C NMR chemical shifts in ppm

relative to TMS as internal standard. The GIAO approach allows the computation of the

absolute chemical shielding due to the electronic environment of the individual nuclei and

this method is often more accurate than those calculated with other approaches for the same

basis set [1]. Gauss View molecular visualization program has been used for the animation

of vibrational band assignments and preparation of the spectrum [50].

1

13

4. Conclusion

The crystal structure of compounds I and II were successfully synthesized and character-

ized by X-Ray Crystallography analysis, FT-IR, and NMR spectroscopy. In the crystal, the

main molecules with the water molecules were connected into a centrosymmetry dimer

in compound I, whereas in compound II, the molecules were linked into one-dimensional

column. The C—H . . . π interactions were also observed in both molecules. The ground

state geometries of the structure were optimized using DFT/B3LYP6-31G+(2d,p) and

DFT/B3LYP6-311G+(2d,p) basis sets and further used to calculate the vibrational frequen-

cies and the isotropic chemical shift. All the calculated values were in a good agreement

with the experimental results. The calculated values from the DFT/B3LYP6-311G+(2d,p)

basis set gave better agreement as compared to the DFT/B3LYP6-31G+(2d,p) basis set.

The observed intermolecular interactions in the crystal packing are the main cause of the

torsion angles differences where these interactions are not taken into consideration during

the optimization process. The differences are also observed in the calculated molecular

vibrations and chemical shifts. In theoretical FTIR and NMR analysis, the atoms involved

in the intermolecular hydrogen bond show a signiﬁcant difference in the wavenumber and

chemical shift values, respectively, compared with the observed data. The correlation values

of 0.995, 0.996, and 0.997 were obtained from the vibrational frequency studies. We hope

that the proposed results can assist others in the experimental and theoretical studies that

are related to the title compounds I and II, where both compounds have been calculated in

the presence of water molecules.

174

I. A. Razak et al.

Supplementary Material

Crystallographic data (excluding the structure factors ﬁle) have been deposited with the

Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB221EZ, UK

(

fax: +44-1223-336033; email: deposit@ccdc.cam.ac.uk or http://www.ccdc.cam.ac.uk) as

supplementary publication no. CCDC 944766 for compound I and 944767 for compound

II.

Acknowledgments

The authors thank the Malaysian Government and Universiti Sains Malaysia (USM) for

the research facilities and USM Short Term Grant, No. 304/PFIZIK/6312078 and FRGS

Grant 59178 to conduct this work. SA thanks the Malaysian government and USM for the

Academic Staff Training Scheme Fellowship (ASTS).

References

[

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Article Doi

Synthesis, Characterization, and Structural Investigations of 1-(3-morpholinopropyl)-3-(4-chlorobenzoyl)thiourea monohydrate and 1-(3-morpholinopropyl)-3-(4-methylbenzoyl)thiourea monohydrate

DOI: 10.1080/15421406.2014.990786

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