DOCKING AND SPECTROSCOPIC (FT-IR, FT- RAMAN ...adalyajournal.com/gallery/33-nov-2244.pdf · Nitrogen and Oxygen in heterocyclic organic compounds evoke drastic changes in its biological

DOCKING AND SPECTROSCOPIC (FT-IR, FT-

RAMAN), COMPUTATIONAL (DFT)

INVESTIGATION, HOMO-LUMO, AND MEP

ANALYSIS OF 4-MORPHOLINECARBONYL

CHLORIDE

K. Venkateswarana, M. Karnanb and R. Muthukumarb

a Future School Auroville 605 101, Tamilnadu, India

b PG & Research Department of Physics, Srimad Andavan Arts and Scinece college,

Tiruchirappali 620 005, India.

Abstract

The FT-IR, FT-Raman spectra of the title molecule 4-Morpholinecarbonyl chloride is

recorded in the range 4000–100 cm-1and 4000–500 cm-1 respectively. All computations were

carried out by DFT methods using the B3LYP/6-311++G (d,p) basis set. The vibrational

fundamental modes of the molecule identified from the spectra, in comparison with computed

wave numbers, were assigned. The different possible donor and acceptor electronic molecular

orbitals were determined using the NBO analysis. The HOMO-LUMO energy distribution

was calculated and the oscillator strength of different bonding and anti-bonding orbitals were

computed, from which the UV-visible spectrum of the molecule, recorded in the range of

200–1100 nm, was explored as to what transition have the peaks in the spectrum. The NMR

chemical shift spectra were recorded in the region 0-12 ppm for hydrogen’s and 0-200 ppm

for carbons. The shifts were also computed using the DFT methods and the values are

compared and assigned for different atoms in the molecule. The reactivity of the molecule

was also investigated and both the positive and negative centers of the molecule were

identified using chemical descriptors and molecular electrostatic potential (MEP) analysis.

The non-linear optical (NLO) properties of the title molecule were identified using the

calculated values of polarizability and hyperpolarizability. The Docking of the molecule with

different protein is carried out in order to understand the biological activity of the molecule.

Key words: FT-IR, FT-Raman, NBO, NLO, UV-Visible, Molecular Docking.

Corresponding author: [email protected]

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Volume 8, Issue 11, November 2019

mailto:[email protected]

3.4 3.2 3.0 2.8 2.6 2.4 2.2 2.0 1.8 1.6

0.0

0.5

1.0

1.5

de

ge

na

rac

y

Chemical shift (PPM)

INTRODUCTION

Morpholine compounds and its derivatives are the fundamental units in the branch of

Medicinal chemistry due to their characteristics Morpholine derivatives play a vital role in

the drug design field which enrich the research activities in the biological field [1]. A vast

Literature studies reveals that Morpholine compound and its derivatives are having very

essential biological activity in different therapeutic areas such as anticancer, antifungal and

antimicrobial etc.,[2] It is well clear that the substituent of electronegativity atoms such as

Nitrogen and Oxygen in heterocyclic organic compounds evoke drastic changes in its

biological properties and it is determined by sigma bond and by SP2 hybridization[3]. The

Morpholine compound containing Nitrogen atom undergoes many chemical reactions like

acylation, Protonation and alkylation [4]. To the best of our knowledge so far no quantum

chemical calculations and molecular docking studies done on 4-Morpholinecarbonyl chloride

[4MCCL]. In the present study Structural, electronic and biological properties studied by

Molecular Geometry, NMR, and HOMO-LUMO and by Molecular docking analysis [5].

Optimized Molecular geometry obtained for 4MCCL by using quantum chemical calculations

which was utilized to do NBO analysis. Herein detailed observation of FT-IR and FT-Raman

theoretical and experimental spectrum are reported both are complementary to each other [6].

It is also decided to have theoretical and experimental determination of Mulliken charge, UV

and NMR analysis of the studied compound by using quantum chemical calculation methods

with a higher basis set.

The aromaticity of the title compound associated with the cyclic delocalization of

electrons giving stability to the compound which was validated by NBO analysis. In the

present investigation we put an effort to study the thermodynamic parameters and NLO

properties like dipole moment, polarizability and Hyper polarizability of pharmacologically

active compound [4MCCL] by DFT method using B3LYP level employing a higher basis set

6-311++G(d,p) in the Gaussian software[7]. Molecular electrostatic potential map, Hardness,

Softness, Chemical potential, Electrophilicity index and HOMO – LUMO energy gap are

calculated by DFT calculations in Gas phase. Molecular docking analysis done on 4MCCL

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to study the main biological function of a Nitrogenous base nucleic acid in the title compound

as they are the building blocks of DNA and RNA which draw main attention to do further

investigation in Morpholine compounds and its derivatives.

1. EXPERIMENTAL DETAILS

The spectra of the compound under investigation namely 4-Morpholinecarbonyl

chloride was purchased from spectral library of Sigma Aldrich chemicals, U.S.A. The FT-IR

spectrum of the compound is recorded in Bruker IFS 66V spectrometer in the range of 4000-

100 cm-1. The spectral resolution is ± 2cm-1. The FT-Raman spectrum of same compound is

also recorded in the same instrument with FRA 106 Raman module equipped with Nd: YAG

laser source operating at 1.064 µm line widths with 200mW power. The spectra are recorded

in the range of 4000-500 cm-1 with scanning speed of 30cm-1 min-1 of spectral width 2 cm-1.

The frequencies of all sharp bands are accurate to ± 1cm-1.

2. COMPUTATIONAL METHODS

The molecular parameters of 4-Morpholinecarbonyl chloride in the ground state are

computed by performing DFT (B3LYP) with 6-311++G(d,p) basis sets. In DFT methods,

Becke’s three parameter exact exchange-functional (B3) [8] combined with gradient-

corrected correlation functional of Lee, Yang and Parr (LYP) [9-10] was chosen for their best

predicting results for molecular geometry and vibrational modes for moderately larger

molecule [11-12]. The minimum energy of geometrical structure is obtained by using same

level of theory. All the computations have been done by adding polarization function ‘p’ and

diffuse function ‘d’ on heavy atoms [13-16], For NMR calculations, the title molecule was

firstly optimized at 6-311++G(d,p) level. After optimization, 1H and 13C NMR chemical

shifts were calculated using the GIAO method in chloroform at DFT method with 6-

311++G(d,p) basis set [17]. TD-B3LYP was used to obtain absorption wavelengths max and

excitation energy, dipole moment and frontier molecular orbital energies. DFT calculations

for 4-Morpholinecarbonyl chloride were performed using GAUSSIAN 09W program

package on Pentium IV processor personal computer. The assignments of the wave numbers

are done by animation option of Gauss View 3.0 [18], a graphical interface of GAUSSIAN

program. Docking analysis was using auto dock software.

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3. RESULTS AND DISCUSSION

4.1 MOLECULAR GEOMETRY

The title molecule has 17 atoms with the molecular formula C5H8O2N1Cl1. The

minimum energy configuration of the title molecule was again optimized at B3LYP/6-

311G++ (d, p) level. The optimized structure of the compound is shown in Fig. 1 and the

optimized structural parameters; bond lengths and bond angles are presented in Table. 1.

From the theoretical values; it is found that most of the optimized bond lengths are slightly

larger than the experimental values. In the case of Morpholine ring, it is observed that the

entire C-H bond in both rings show almost same value (1.085+.005) Å. which indicates that

the C-H bond lengths are not subjected to any external influence. But, the C-C bond lengths

are 1.52 & 1.52 Å for C1-C2 and C3-C4 which are inside the ring. These values are much

higher than the expected value [19] due to substituent of Oxygen and Nitrogen atoms. While

other bond length values are lies in expected range.

Bond angles of the carbon atoms in the benzene ring are around 1200. All the angles

are varying in between 1080 to 1270 because of the substituted chlorine atom. Moreover, the

changes in bond angle values indicate that the presence of O atom in the nearby functional

groups have considerably changed the hybridization of the carbon atoms. The dihedral

angles of the title compound mostly like below 150 º due to the distortion of SP2 & SP3

hybridization [20]. The difference between the values is due to the effect of steric repulsions,

substituent and conjugation.

Fig. 1. Molecular analysis of 4-Morpholinecarbonyl chloride

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Table. 1. The calculated geometric parameters of 4-Morpholinecarbonyl chloride.

Bond length Bond Angle Dihedral Angle

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

C1-C2 1.52

C2-C1-N5 109.4

N5-C1-C2-H7 67.47

C1-N5 1.46

C2-C1-H6 109.6

N5-C1-C2-O10 -54.67

C1-H6 1.09

C2-C1-H17 110.2

N5-C1-C2-H16 -172.8

C2-H17 1.08

N5-C1-H6 108.8

H6-C1-C2-H7 -173.1

C2-H7 1.09

N5-C1-H17 109.8

H6-C1-C2-O10 64.73

C2-O10 1.42

H6-C1-H17 108.6

H6-C1-C2-H16 -53.44

C2-H16 1.09

C1-C2-H7 109.7

C2-C1-N5-C4 -53.53

C3-C4 1.52

C1-C2-O10 111.6

C2-C1-N5-C11 -175.6

C3-H8 1.09

C1-C2-H16 110

H6-C1-N5-C4 66.12

C3-O10 1.42

H7-C2-O10 109.9

H6-C1-N5-C11 51.64

C3-H15 1.09

H7-C2-H16 108.7

C1-C2-O10-C3 -137.4

C4-N5 1.47

C4-C3-H8 106.6

H7-C2-O10-C3 -68.27

C4-H9 1.08

C4-C3-O10 109.8

H16-C2-O10-C3 102.6

C4-H14 1.09

C4-C3-H15 111.4

H8-C3-C4-N5 172.9

N5-C11 1.35

H8-C3-O10 110.1

H8-C3-C4-H9 -16.14

C11-O12 1.19

H8-C3-H15 109.8

H8-C3-C4-H9 59.82

C11-CL13 1.82

C3-C4-N5 108.7

H8-C3-C4-H14 -62.22

C3-C4-H9 106.6

O10-C3-C4-N5 -179.9

C3-C4-H14 109.5

O10-C3-C4-H9 -67.34

H9-C4-H14 111.1

O10-C3-C4-H14 52.76

N5-C4-H9 109.8

H15-C3-C4- N5 173.1

N5-C4-H14 108.6

H15-C3-C4- H9 54.71

H9-C4-H14 108.8

H15-C3-C4-H14 174.8

C1-N5-C4 108.7

C4-C3-O10-C2 -64.8

C1-N5-C11 113.7

H8-C3-O10-C2 172.8

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C4-N5-C11 127.7

H15-C3-O10-C2 -67.04

C2-O10-C3 117.8

C3-C4-N5-C1 53.32

N5-C11-O12 111.1

C3-C4-N5-C11 -59.81

N5-C11-CL13 127.3

H9-C4-N5-C1 62.24

O12-C11-CL13 114.1

H9-C4-N5-C11 179.9

H14-C4-N5-C1 -51.81

H14-C4-N5-C11 136.2

C1-N5-C11-O12 -173.3

C1-N5-C11-CL13 14.69

C4-N5-C11-O12 68.35

C4-N5-C11-CL13 -103.5

4.2 MULLIKEN POPULATION ANALYSIS AND NAC METHOD

The atomic charge analysis plays a substantial role in the quantum chemical

calculations which can influence the properties of the molecular system, such as its dipole

moment, bond strength, vibrational frequencies, electronic transitions, chemical shifts and

molecular polarizability etc. Moreover, these charges are useful in determining the biological

activity. The biological activity increases with increasing charge on atom [21]. The atomic

charges were calculated by two methods for comparison purpose; Mullikan Population

analysis (MPA) and Natural atomic charges (NAC) methods.

Both Mullikan and Natural atomic charges of the title compound were computed by

B3LYP/6-311++G(d,p) method and the values are presented in the Table.2. Carbon atoms in

the morpholine rings for both the charges are expected to be equally negative. In C1 (-0.238),

C2 (-0.36), C3 (-0.351) and C4 (-0.262) lies in expected level. But C11 is observed high

positive (0.626) in NAC. The NAC prediction seems to be valid as the carbon atom is

attached only with N, Cl, O atom. It is reasonable that the reduction in the positive value with

respect to the expected value. On the other side of the chlorine atom (CL 13), reflects that it

can be highly positive value.

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Fig. 2. Mulliken Charge and Natural charge for 4-Morpholinecarbonyl chloride

Table. 2.

Mulliken Charges of 4-Morpholinecarbonyl chloride Computed at B3LYP/6-

311++G(d,p) basis set.

Atoms Mulliken Atomic Charge

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

Natural atomic Charge

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

C1 -0.23868 -0.21074

C2 -0.36987 -0.02149

C3 -0.3512 -0.02299

C4 -0.26282 -0.19958

N5 0.179328 -0.53558

H6 0.172325 0.18216

H7 0.149908 0.1638

H8 0.149942 0.16376

H9 0.194825 0.22553

O10 -0.14056 -0.59741

C11 -0.33774 0.62628

O12 -0.20528 -0.56812

Cl13 0.34068 0.00896

H14 0.202518 0.18594

H15 0.191865 0.19288

H16 0.194561 0.19079

H17 0.130195 0.21582

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4.3 NMR ANALYSIS

Chemical shielding calculations are fast, accurate and applicable for complex systems.

The chemical shifts for 1H and 13C atoms of the titled compound were computed for

optimized structure, supported by GIAO method. The computed chemical shift values in gas

and solvent phase and experimental values at CDCl3 solvent are presented in Table.3.

1H NMR spectra

The 1H NMR spectra (both theoretical and experimental) are shown in Fig.3 and 4.

The 1H NMR spectra interpreted significantly in an attempt to measure the possible different

effects appearing on the chemical shift values of proton. [22] The usual scale, for PMR

(Proton Nuclear Magnetic resonance) studies is about 10ppm. In the present study, all the

theoretical HNMR chemical shift values are in not good agreement with experimental values.

1H NMR chemical shifts in the ligand ring protons i.e., for H6, H7, H8 H9, H14, H15, H16, H17

are in between 1.78 - 3.24 ppm respectively.

13C NMR spectra

The 13C NMR spectra (both theoretical and experimental) are shown in Fig. 4. The

titled compound showed the chemical shifts of carbon atoms in benzene rings as well as in

aldehyde and methoxy groups. This chemical shift values for aromatic ring carbon atoms are

expected between 120 - 130 ppm: around 120 ppm in gas phase and 130ppm in solvent phase

[23]. In C11 atom has high chemical shift range due to the influence of O, N, CL atoms. On

the other hand C1, C2, C3, C4 atoms are between 51.9 - 68.5 ppm.

Table. 3. Values of Atom Gas Chloroform for 4-Morpholinecarbonyl chloride

ATOM GAS Chloroform EXP. ATOM GAS Chloroform EXP.

1C 51.9 51.9 41.1 6H 1.78 1.78 1.98

2C 68.0 68.5 65.9 7H 2.79 2.79 2.80

3C 68.5 68.5 65.9 8H 2.82 2.82 2.81

4C 54.3 54.3 48.4 9H 3.24 3.24 3.26

11C 195.0 195.0 147.5 14H 1.91 1.91 1.91

15H 3.24 3.24 3.28

16H 3.22 3.22 3.21

17H 2.94 2.94 2.98

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i

-114 13 12 11 10 9 8 7 6 5 4 3 2 1 0 ppm

-0.103

-0.092

0.696

1.091

1.976

1.982

1.994

2.002

2.009

2.898

2.985

3.086

3.218

3.288

3.365

3.724

3.840

4.056

4.085

4.453

7.261

9.814

11.642

12.719

0.12

0.27

0.06

1.00

1.19

1.37

1.91

1.19

1.58

0.96

0.36

0.09

0.15

0.15

Current Data ParametersNAME V-2

EXPNO 1PROCNO 1

F2 - Acquisition ParametersDate_ 20190402Time 13.16

INSTRUM spectPROBHD 5 mm BBO BB-1HPULPROG zg30

TD 65536SOLVENT CDCl3NS 16

DS 2SWH 8223.685 HzFIDRES 0.125483 Hz

AQ 3.9846387 secRG 32DW 60.800 usec

DE 6.00 usecTE 292.6 KD1 1.00000000 sec

TD0 1

======== CHANNEL f1 ========

NUC1 1HP1 14.35 usec

PL1 -1.00 dBSFO1 400.1324710 MHz

F2 - Processing parametersSI 32768SF 400.1300093 MHz

WDW EMSSB 0LB 0.30 Hz

GB 0PC 1.00

PROTON CDCl3 {D:\CIF} CIF_NMR 1

Fig. 3 Experiment NMR chemical shift 4-Morpholinecarbonyl chloride

200 180 160 140 120 100 80 60 40 20 ppm

46.17

48.41

65.68

65.96

76.84

77.16

77.48

147.84

Current Data ParametersNAME V-2EXPNO 2PROCNO 1

F2 - Acquisition ParametersDate_ 20190402Time 13.18INSTRUM spectPROBHD 5 mm BBO BB-1HPULPROG zgpg30TD 65536SOLVENT CDCl3NS 194DS 4SWH 24038.461 HzFIDRES 0.366798 HzAQ 1.3631988 secRG 322DW 20.800 usecDE 6.00 usecTE 292.7 KD1 2.00000000 secd11 0.03000000 secDELTA 1.89999998 secTD0 1

======== CHANNEL f1 ========NUC1 13CP1 9.95 usecPL1 -1.00 dBSFO1 100.6228298 MHz

======== CHANNEL f2 ========CPDPRG2 waltz16NUC2 1HPCPD2 90.00 usecPL12 14.95 dBPL13 120.00 dBPL2 -1.00 dBSFO2 400.1316005 MHz

F2 - Processing parametersSI 32768SF 100.6127977 MHzWDW EMSSB 0LB 1.00 HzGB 0PC 1.40

1H NMR-Experimental

13C NMR-Experimental

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200 180 160 140 120 100 80 60 40

0.0

0.5

1.0

1.5

de

ge

ne

rcy

chemical shift (ppm)

3.4 3.2 3.0 2.8 2.6 2.4 2.2 2.0 1.8 1.6

0.0

0.5

1.0

1.5

de

ge

na

rac

y

Chemical shift (PPM)

Fig. 4. Theoretical NMR chemical shift 4-Morpholinecarbonyl chloride

4. VIBRATIONAL ANALYSIS

The titled molecule under investigation has 17 atoms and has 46 normal modes of

fundamental vibrations. Vibrational wave numbers for all the fundamental modes of the titled

compound were computed using DFT (B3LYP) methods with 6-311++G (d,p) basis set and

the values along with the experimental values are presented in Table 4. The experimental and

theoretical spectra of the titled compound are shown in Fig. 5 and 6, respectively.

By observing the experimental and theoretical frequencies, the theoretical values were

slightly higher than the experimental values for the majority of the normal modes, comes to

the conclusion that two factors may be responsible for the discrepancies between the

experimental and computed wave numbers; the first is caused by the unpredictable electronic

distribution among the different bonds in the molecule and the second reason is the

anharmonic nature of the vibrations which cannot be accounted completely by the theory. To

make coincidence with experimental and theoretical data, scaling strategies were utilized.

5.1 CH Vibrations

In the aromatic compounds, the C-H stretching normally occurs in the region of 3100-

3000 cm-1 [24]. For the title molecule, there are eight CH stretching vibrations of Morpoline

rings, which are theoretically observed at 3250, 3247, 3244, 3241, 3181, 3180, 3178 and

3174 cm-1, all these are found completely within the range which shows they are not affected

by the substitutional groups, as predicted in the earlier analyses. There are six CH bonds in

the aliphatic groups; five in methoxy and one in aldehyde groups respectively. Some values

are pushed up and some are pulled down, these are impact observed as due to the influence of

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O atoms in the methoxy and aldehyde groups on the CH stretching vibrations. The entire

aromatic C-H stretch mode is pure stretching modes as it is evident from PED values.

Normally the strongest absorptions for in-plane and out of plane bending CH

vibrations occur in the region 1300-1000 cm-1 and 1000-750 cm-1 respectively [25-26]. The

distinction between the aromatic and aliphatic among bending vibrations will not be there. In

the title compound, the in-plane bending vibrations are found at 1267 and 1198 cm-1 at IR

region and 1295, 1278, 1250 and 1103 cm-1 at FT- Raman. Theoretically, these vibrations are

observed in the range 1326 to 1109 cm-1. These values show entire vibrations are observed at

the middle of the expected region, hence there is no visible influence of O atoms in the CH

bending modes.

CC Vibrations

The ring stretching vibrations are very much important in the spectrum of benzene

and its derivatives. The bands between 1600-1400 cm-1 in are usually assigned to benzene

CC modes, particularly 1600-1500 cm-1 to C=C [27] and 1500-1400 cm-1 to C-C modes[28],

even though no such clear distinction occurs as C=C and C-C within the rings due to

electronic conjugation. However, the vibrations can be taken to be closer to double bond and

single bond CC, as the electronic distribution is not entirely uniform among these bonds. In

the present compound, two stretching vibrations can be assigned to 1444 cm-1 in FT-Raman

within the rings. Theoretically, the CC stretching vibrations are observed at 1445-1434 cm-1

respectively. All these values are exactly as they should be except a few values which are

found above and below the expected ranges.

CN & C-CL Vibrations

In the vibrational modes CN usually assign 1400-1200cm−1 [29]. In present

morpholine compound existing 1404 cm−1 in FT-Raman spectrum while the observed CN

stretching band at the range of 1434, 1423 and 1421 cm−1 in theoretically. It's very high due

to the attachment of electronegative atoms. The PED analysis for the title compound shows

that C-O stretching vibration with a vibrational assignment of normal interacting well with

the bending CNC vibrations.

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Normally CL vibrational modes CCL usually assign 850–550 cm-1 [30]. In present

case this compound assigned at 510 cm−1 spectrum in theoretical range and 581 in FT- IR

spectrum. This range is lies in the expected range. Whereas the in and out of plane bending

vibration's are also assigned in the expected range.

CO Vibrations

As per the previous literatures, the CO bond is expected in the region 1220-970 cm−1

[31]. In the present molecule, the C=O stretching band is observed at FT-IR 1361 cm−1 and

1331, 1295 cm−1. Theoretical wave number of this mode is 1351, 1344 and 1326 cm−1. This

values lie at the higher end of the expected range. It seems the CO modes in this molecule are

boosted by sharing energy with CH modes. The in-plane bending mode based on the PED

contribution is assigned though it is expected to be with in-plane bending modes of C-O,

whose in-plane and out of plane bending modes are expected in the range 625±70 cm-1 and

540±80 cm-1 respectively. C-O stretching is observed in expected range. These ranges are

lies in literatures range.

4000 3500 3000 2500 2000 1500 1000 500

2000

1500

1000

500

0

Inte

nsity

wavenumber cm-1

B

Fig. 5 Theoretical FT-IR and FT-Raman spectra 4-Morpholinecarbonyl chloride

4000 3500 3000 2500 2000 1500 1000 500

0

2

4

6

8

10

Inte

nsity

Wavenumber (cm-1)

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3500 3000 2500 2000 1500 1000 500

0

5000

10000

15000R

am

an

In

ten

sity

Wave number (cm-1)

Fig. 6 Experimental FT-IR and FT-Raman spectra 4-Morpholinecarbonyl chloride

6. OTHER ANALYSIS

6.1 NBO Analysis

The bonding and non-bonding (anti-bonding) interactions can be quantitatively

described in terms of the NBO analysis and is tabulated in Table.5. In this study, the charges

transferring from bonding to anti-bonding levels were analyzed [32]. The intra-molecular

hyper conjugative interactions are caused by the orbital overlapping between σ and π (C-C,

C-O, C-H, C-N, C-Cl) bond orbitals. The highest stabilization energy of the title molecule are

O12 to C11-Cl13 (n- π*, 33.27 kcal/mol), O12 to N5-C11 (n- π*, 19.65 kcal/mol), N5 to

C11-O12 (n- π*, 15.9 kcal/mol), CL13 to C11-O12 (n- π*, 14.02 kcal/mol), CL13 to N5-C11

(n- π*, 6.48 kcal/mol).

Table.4. Observed method B3LYP/6-311++G (d,p) level calculated Vibrational

frequencies of 4-Morpholinecarbonyl chloride

Experimental frequency

(cm-1) B3LYP/6-311++G(d,p)

Calculated

frequency(cm-1)

B3LYP/6-311++G (d,p) VEDA %

FT-IR FT-RAMAN Unscaled

(cm-1)

Scaled

(cm-1)

3317 3250.66 ν– CH 92%

3314 3247.72 ν– CH 99%

3311 3244.78 ν– CH 90%

3308 3241.84 ν– CH 98%

3246 3181.08 ν– OC 78%, NC 11%

3245 3180.1 ν– CC 62%

3243 3178.14 ν– CC 85%

3239 3174.22 β–HCC 80%

1449 1444 1475 1445.5 β–HCC 76%

1440 1464 1434.72 ν– NC 38%, β–HCC 25%

1453 1423.94 ν– NC 23%, β–CNC 13%,HCC 26 %

1450 1421 β–,HCC 78 %

1361 1430 1401.4 ν– NC 22%, OC 15%, β–HCC 14 %

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1331 1351 1323.98 ν– OC 49%, β–HCC 11 %

1344 1317.12 ν– NC 10%, β–CCN 37 %, CCO 28%

1295 1326 1299.48 ν– OC 72%

1306 1279.88 τ– HCCH 96%

1278 1302 1275.96 τ– HCCH 93%

1267 1250 1275 1249.5 ν– CLC 10%, β–CNC 17 %, OCCL 23%,COC 21%

1263 1237.74 γ– CCOH 92%

1198 1197 1173.06 τ– HCCO 90%

1169 1145.62 β–CCN 15%, CCO 51%

1103 1109 1086.82 ν– NC 24%,CLC12%, β–COC 22 %, NCCL11%

1%11111123%,COC 21% 1084 1062.32 τ– NCCO 10%, γ– ONCLC 76%

1066 1057 1035.86 τ– NCCO 74%, γ– ONCLC 16%

1012 1045 1024.1 β–OCCL 16%,CNC 18%,COC 23%,NCCL 15%

938 1018 997.64 τ– NCCO 92%,

913 966 946.68 ν– CLC 54%, β– OCCL 27 %

911 892.78 ν– CLC 15%, β–CNC 32%, OCCL 17 %

870 877 859.46 β–CNC 46%, NCCL 46%

760 824 807.52 τ– CCOC 11%, γ– CCCN 74%

700 790 774.2 τ– CNCCL 76%, γ– CCCN 12%

657 762 746.76 τ– CCOC 82% 625 660 646.8 β–CNC 13%,

587 522 511.56 CNC 18%,COC 23%,NCCL 15%

498 491 481.18 ν– NC 24%,CLC12%, β–COC 22 %, NCCL11%

1%11111123%,COC 21% 464 428 419.44 τ– NCCO 10%, γ– ONCLC 76% 442 424 415.52 ν– CLC 54%, β– OCCL 27 %

346 339.08 ν– CLC 15%, β–CNC 32%, OCCL 17 % 310 303.8 γ– CCOH 92% 258 252.84 τ– HCCO 90% 211 206.78 ν– CLC 10%, β–CNC 17 %, OCCL 23%,COC 21%

103 100.94 ν– NC 22%, OC 15%, β–HCC 14 % 56 54.88 ν– OC 49%, β–HCC 11 % 51 49.02 ν– NC 10%, β–CCN 37 %, CCO 28%

ν–stretching; β–in–plane bending; δ–deformation; ρ–rocking; γ–out of plane bending; ω–

wagging and τ–torsion. IR and Raman intensities are normalized to 100.

Table: 5

Donor

Type of

bond Occupancy Acceptor

Type of

bond Occupancy E2

e E(j)-

E(i) F(I,j)

O 12 n 1.825 C 11 -Cl 13 π * 0.132 33.27 0.38 0.102

O 12 n 1.825 N 5 - C 11 π * 0.092 19.65 0.57 0.097

N 5 n 1.788 C 11 - O 12 π* 0.231 15.91 0.38 0.07

Cl 13 n 2.001 C 11 - O 12 π* 0.231 14.02 0.38 0.067

Cl 13 n 2.001 N 5 - C 11 σ* 0.092 6.48 0.62 0.057

Cl 13 n 2.001 C 11 - O 12 σ* 0.068 5.87 0.74 0.059

O 10 n 1.999 C 1 - C 2 σ* 0.027 5.4 0.65 0.054

O 10 n 1.999 C 3 - C 4 σ* 0.024 5.35 0.66 0.054

N 5 n 1.999 C 1 - H 6 σ* 0.024 5.28 0.76 0.059

O 10 n 1.999 C 2 - H 7 σ* 0.027 5.22 0.71 0.055

O 10 n 1.999 C 3 - H 8 σ* 0.026 5.2 0.71 0.055

N 5 n 1.999 C 4 - H 14 σ* 0.022 5.01 0.76 0.058

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C 4 - N 5 σ 1.973 C 11 -Cl 13 σ* 0.132 3.95 0.83 0.053

C 4 - H 9 σ 1.978 C 3 - O 10 σ* 0.091 3.43 0.81 0.047

C 1 - H 17 σ 1.978 C 2 - O 10 σ* 0.013 3.28 0.82 0.046

C 4 - H 9 σ 1.978 C 1 - N 5 σ* 0.024 3.1 0.84 0.046

N 5 n 1.788 C 11 - O 12 σ* 0.068 3.05 0.75 0.044

C 3 - H 15 σ 1.987 C 4 - N 5 σ* 0.022 3.02 0.85 0.045

C 1 - H 17 σ 1.978 C 4 - N 5 σ* 0.022 2.98 0.86 0.045

C 2 - H 16 σ 1.982 C 1 - N 5 σ* 0.037 2.95 0.85 0.045

C 3 - C 4 σ 1.825 N 5 - C 11 σ* 0.092 2.77 0.91 0.046

C 3 - H 15 σ 1.981 C 2 - O 10 σ* 0.019 2.65 0.82 0.041

C 2 - H 16 σ 1.982 C 3 - O 10 σ* 0.019 2.63 0.82 0.041

C 1 - C 2 σ 1.986 N 5 - C 11 σ* 0.092 2.48 0.91 0.043

C 2 - H 7 σ 1.986 C 1 - H 6 σ* 0.024 2.35 0.95 0.042

C 3 - H 8 σ 1.986 C 4 - H 14 σ* 0.022 2.3 0.95 0.042

Cl 13 n 1.991 C 11 - O 12 π* 0.231 2.12 0.38 0.026

C 1 - N 5 σ 1.977 C 11 - O 12 π* 0.068 2.08 0.77 0.038

C 4 - H 14 σ 1.984 C 3 - H 8 σ* 0.025 2.03 0.94 0.039

C 1 - H 6 σ 1.986 C 2 - H 7 σ* 0.025 2 0.95 0.039

C 3 - C 4 1.987 N 5 - C 11 σ* 0.079 2.03 1.22 0.045

6.2 UV-Visible Analysis

The UV-Vis absorption spectrum of the titled compound is recorded in the range 200-

400 nm are shown in Fig 7. Theoretical calculations have been investigated in Gas phase and

in organic solvent (ethanol) by TD-DFT method in order to get a deeper insight into the

possible electronic excitations, wavelengths, oscillator strengths and major orbital

contributions of various excitations of the titled compound [33]. The electronic transitions

and the corresponding excitation energies for these two phases are presented in Table 6. The

calculated absorption maxima values are at 321, 269 and 248 nm for gas phase and for

ethanol it was 314, 274 and 258 nm .The experimental absorption maxima is obtained at 319

nm.

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200 300 400

-1.2

-1.0

-0.8

-0.6

-0.4

-0.2

0.0

0.2

0.4

Ab

so

rba

nce

Wavelength (nm)

Fig. 7. UV-Vis Theoretical & Experimental spectrum of 4-Morpholinecarbonyl chloride

Table. 6.

Theoretical electronic absorption spectra of B3LYP/6-311++G (d,p) absorption wavelength λ

(nm), excitation energies E (ev) and oscillator strengths (f) using TD-DFT/B3LYP/6-

311++G(d,p) method.

λ (nm) E(eV) (f) Major contribution

Theoretical Gas Experimental

321.5 3.855 0.0002 HOMO->LUMO (99%)

269.4 4.600 0.0136 HOMO->L+2 (97%)

248.0 4.998 0.3355 HOMO->L+1 (94%)

243.1 5.098 0.0106 HOMO->L+3 (95%)

233.7 5.3036 0.0006 HOMO->L+4 (98%)

218.7 5.668 0.0010 HOMO->L+5 (26%)

214.1 5.790 0.0122 HOMO->L+5 (73%)

204.3 6.068 0.0005 H-1->L+1 (93%)

198.5 6.245 0.0019 HOMO->L+8 (96%)

197.8 6.265 0.0000 HOMO->L+7 (99%)

Ethanol

314.3 319 3.944 0.4314 HOMO->LUMO (97%)

274.1 4.522 0.0090 HOMO->L+2 (98%)

258.3 4.799 0.0112 HOMO->L+1 (94%)

243.7 5.086 0.0234 HOMO->L+3 (96%)

226.0 5.484 0.0000 HOMO->L+4 (98%)

218.3 5.678 0.0049 HOMO->L+5 (97%)

212.3 5.839 0.0002 HOMO->L+6 (95%)

199.6 6.209 0.0005 H-2->L+1 (89%)

199.4 6.217 0.0044 HOMO->L+8 (97%)

197.3 6.281 0.0001 HOMO->L+7 (98%)

6.3 HOMO-LUMO analysis

The energy gap between HOMO and LUMO is used to find the chemical behaviour,

high reactivity, low kinetic stability of the compound. Using B3LYP method, the calculated

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HOMO and LUMO energies of the titled molecule is -7.86 and -0.77eV, respectively, and the

energy gap between them is -7.09 eV. The HOMO-LUMO energy gap and different

reactivity descriptors of the molecule in both levels are presented in Table 7. The negative

surface was represented as red and the positive charges were represented by blue color. The

low HOMO-LUMO energy gap reveals the ultimate possible charge transfer within the

molecule and hence there is the possibility of high chemical and biological reactivity [32].

With respect to the electronic transitions, there are three maximum computed wavelengths at

314, 274 and 258 nm, which correspond to the contribution of HOMO/LUMO (97%),

H/L+2(98%), H/L+1(94%) in the solvent phase. These transitions can be accounted for non-

bonding transition (n- *) of the lone pair in the molecule are shown in Fig.8.

HOMO LUMO

Fig. 8. HOMO-LUMO pictorial plots of 4-Morpholinecarbonyl Chloride

Table: 7

HOMO, LUMO, global electronegativity, global hardness and softness, global

electrophilicity index of B3LYP/6-311++G (d,p).

Parameters Gas

EHOMO (ev) -7.86

ELUMO (ev) -0.77

∆EHOMO-LUMO gap (ev) -7.09

Electronegativity (χ) 4.32

Global hardness (η) 3.55

Global softness (S) 14.18

Chemical Potential 2.63

Dipole moment(µ) 3.439

6.4 MEP Analysis

The MEP map for the title molecule is as shown in Fig 9. and the different values of

MEP surface are represented by different colors: red, blue and green which indicates the

regions of most negative, most positive and zero electrostatic potential, respectively [33-34].

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It is evident that the maximum negative region (electrophilic) shown in red color at the C=O

site is the strongest affinity for a proton while the maximum positive region (nucleophilic)

referred in blue color around the hydrogen atoms is the strongest affinity for electron. The

positive and negative potential of the molecule ranges from -4.703e-2 au. To +4.703e-2 au.

Fig. 9. Molecular electrostatic potential of 4-Morpholinecarbonyl Chloride

6.5 NLO properties

Natural and semi-natural NLO materials have been subjected to intense research due

to their possible applications in wide range of automations, such as optical communication,

optical computing and data storage, etc. The first order hyperpolarizability is a third rank

tensor that can be designated by a 3x3x3 matrix [35]. The NLO properties of 4-

Morpholinecarbonyl chloride compound were calculated using 6-311++G(d,p) method. The

electronic dipole moment (µ) (Debye), polarizability (α) and first hyperpolarizability (β) of 4-

Morpholinecarbonyl chloride are given in table 8. Standard value for urea (μ=1.3732 Debye,

β0=1.584x10-30esu): esu-electrostatic unit. The dipole moment (µ) and first order

hyperpolarizability (β0) values are calculated at 3.439 Debye and 15.65 *10-33esu,

respectively. These results show that, the βo calculated values of molecules are higher than

the magnitude of urea which is used frequently as a threshold value for comparative

determinations. This high range of hyperpolarizability can be obtained by the presence of

electro-negative nitro group and π bonds. The theoretical computed of β components is very

useful as this clearly represents the charge delocalization direction. Domination of individual

element indicates on a substantial charges delocalization in this direction. The βxxx direction

described the largest range of hyperpolarizability which insists that the electron cloud

delocalization is more that direction than other directions. Therefore, the largest βxxx value

indicates charge delocalization is perpendicular to the bond axis and the involvement of π

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orbitals in intra-molecular charge transfer process. Hence the molecule has good NLO

activity.

Table 8.

The electronic dipole moment (µ) (Debye), polarizability(α) (in a.u) and first

hyperpolarizabiliy (β) components and βtot (10-30 esu) value of 4-Morpholinecarbonyl

chloride

Parameter a.u. Parameter a.u.

α xx -63.6275 βxxx 11.3970

αxy -7.3612 βxyy -18.3722

αyy -55.4136 βxzz 7.3631

αxz 1.4076 βyyy -12.7196

αyz -61.0916 βyxx -3.1227

αzz 0.1469 βyzz 0.9387

α tot -39.631*10-24esu βzzz 2.3737

∆α 122.37*10-24esu βyyz -2.3913

µx -1.4794 βxxz -4.7534

µy -1.8343 βxyz -0.6451

µz -0.5838 βtot 15.65*10-33 esu

µtot 2.4277

6.6 Thermodynamic analysis

The thermodynamic functions of this 4-Morpholinecarbonyl chloride molecule at

different temperatures were calculated at B3LYP/6-311++G(d,p) level and were listed in the

Table.9. The entropy, specific heat capacity and enthalpy were varied with respect to

temperature from 100K to 300K.The variation of the parameters was found to be linear and

sustained up to the maximum temperature. This shows that the consistent chemical stability

of this compound. Similarly, the free energy of Gibbs was observed to be linear with respect

to temperature. The chemical reaction can be possible when the free energy of Gibbs of the

molecular system decreases. It indicates that the free energy of Gibbs may be negative or less

than zero; the chemical reaction is continued [36]. If it is positive, the reaction will be

stopped. In this case, the Gibbs energy was observed to be still negative up to 300K and it

was resolved that, the present compound was chemically strong and active.

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Table: 9

Thermo dynamical properties at different temperature at the B3LYP/6-311++G(d,p)

level of 4-morpholine carbonyl chloride

T(K) )K mol(cal -1-1C )K mol(cal -1-1S )mol(kcal -1H

100 12.03 65.95 53.86

200 20.13 78.07 55.46

300 29.27 88.84 57.95

100 150 200 250 300

10

20

30

40

50

60

70

80

90

Temp (K)

Heat Capacity

Entropy

Enthalpy

Fig.10. Thermo dynamical analysis of 4-morpholinecarbonyl chloride

6.7 Docking Analysis

The study of molecular docking of the present molecule was carried out by Auto

Dock – Vina software and PyMol molecular graphics system [37]. The ligand was chosen by

minimizing its energy at B3LYP/ 6-311G++ (d, p) functionals and basis sets and the online

tool “Pass” is used to predict the different types of biological activities of the title molecule.

In this present study, Escherichia coli (protein ID: 2R9N). Generally, Hydrogen were added

with target protein and therefore Kollman atomic charges were observed and Lamarckian

genetic algorithm (LGA) was used for molecular docking study in Auto Dock software

package. The binding pocket of protein was obtained by grid size of 90 X, 90 Y & 92 Z Å

with the help of Auto grid. By using Auto dock software, the inhibition constants,

intermolecular energy are calculated. The bond distance of the title molecule to the targeted

protein were 1.8 with inhibition constant of three residue (LYS ‘183’) involved in bonding

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https://www.rcsb.org/pdb/search/smartSubquery.do?smartSearchSubtype=TreeEntityQuery&t=1&n=562

with the title compound were obtained using Discover studio visualizer 4.1 software and the

values are tabulated in Table 8. The formation of hydrogen between ligands and protein were

represented by yellow dotted lines in the Fig 10. In addition, the molecule is suggested with

Homo sapiens activity which is consistent with the experimental values.

Fig. 11. Molecular docking of 4-morpholinecarbonyl chloride

Table 8.

Molecular docking analysis of 4-MorpholineCarbonyl chloride

Protein

(PDB ID)

Binding

Energy

No. of

hydrogen

bond

Bonded Residues Bond Distance

2R9N -4.94 1 LYS 183 1.8

6.8 Conclusion

A broad study of FT-IR and FT-Raman spectral analysis and DFT calculations were

carried out on the title compound 4- Morpholinecarbonyl chloride using B3LYP level

with a higher basis set of 6-311++G(d,p). Non-planar nature of [4MCCL] molecule was

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https://www.rcsb.org/pdb/search/smartSubquery.do?smartSearchSubtype=TreeEntityQuery&t=1&n=9606

exposed by molecular geometry optimization. Neither increase nor decrease in C-H bond

lengths in Morpholine and aliphatic rings confirms that they are not subjected to any

external influence which was well explained with the help of Mulliken charge analysis.

NBO analysis quantitatively described the bonding, antibonding and hyper conjugative

interactions which confers the molecular stability. The low HOMO-LUMO energy gap

predicts the possibility of charge transfer occur within the molecule and suggest the high

chemical reactivity of the molecule. The Molecular electrostatic potential and NLO

properties were studied using B3LYP level/6-311++G(d,p) basis set. The electronic

properties of the compound calculated by UV – Vis analysis, similarly the relation

between the thermodynamic parameters with temperature are also studied. The

theoretical and experimental NMR analysis confirmed the Molecular structure of the title

compound. Molecular docking studies reveals that protein 2R9N forms Hydrogen bond

with Morpholine ring which results in Kollman atomic charges, this properties shows that

the title compound has good biological activity.

6.8 Reference

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[16] C.N.R. Rao, Chemical Applications of Infrared Spectroscopy, Academic Press,New

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