Synthesis, vibrational spectroscopic investigations, molecular docking, antibacterial studies and molecular dynamics study of 5-[(4-nitrophenyl)acetamido]-2-(4-tert-butylphenyl)benzoxazole

Article abstract of DOI:10.1016/j.molstruc.2016.12.020

Antimicrobial active 5-[(4-nitrophenyl)acetamido]-2-(4-tert-butylphenyl)benzoxazole (NATPB) was synthesized and observed IR, Raman bands are compared with the theoretically predicted wave numbers. In the IR spectrum the NH stretching wave number splits in

Full text of DOI:10.1016/j.molstruc.2016.12.020

Accepted Manuscript
Synthesis, vibrational spectroscopic investigations, molecular docking, antibacterial
studies and molecular dynamics study of 5-[(4-nitrophenyl)acetamido]-2-(4-tert-
butylphenyl)benzoxazole
Y. Sheena Mary, Mona M. Al-Shehri, K. Jalaja, Fatmah A.M. Al-Omary, Ali A. El-
Emam, C. Yohannan Panicker, Stevan Armaković, Sanja J. Armaković, Ozlem Temiz-
Arpaci, C. Van Alsenoy
PII:
S0022-2860(16)31310-2
10.1016/j.molstruc.2016.12.020
MOLSTR 23218
DOI:
Reference:
To appear in: Journal of Molecular Structure
Received Date: 27 August 2016
Revised Date: 5 December 2016
Accepted Date: 6 December 2016
Please cite this article as: Y. Sheena Mary, M.M. Al-Shehri, K. Jalaja, F.A.M. Al-Omary, A.A. El-Emam,
C. Yohannan Panicker, S. Armaković, S.J. Armaković, O. Temiz-Arpaci, C. Van Alsenoy, Synthesis,
vibrational spectroscopic investigations, molecular docking, antibacterial studies and molecular
dynamics study of 5-[(4-nitrophenyl)acetamido]-2-(4-tert-butylphenyl)benzoxazole, Journal of Molecular
Structure (2017), doi: 10.1016/j.molstruc.2016.12.020.
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Title of the article: Synthesis, vibrational spectroscopic investigations, molecular docking,
antibacterial studies and molecular dynamics study of 5-[(4-nitrophenyl)acetamido]-2-(4-tert-
butylphenyl)benzoxazole

ACCEPTED MANUSCRIPT
Synthesis, vibrational spectroscopic investigations, molecular docking, antibacterial studies
and
molecular
dynamics
study
of
5-[(4-nitrophenyl)acetamido]-2-(4-tert-
butylphenyl)benzoxazole
b
b
Sheena Mary Ya, Mona M.Al-Shehri , K.Jalajac,d, Fatmah A.M.Al-Omary , Ali A.El-
Emamb, C.Yohannan Panickera, Stevan Armakoviće, Sanja J. Armakovićf, Ozlem Temiz-
Arpacig, C.Van Alsenoyh
aDepartment of Physics, Fatima Mata National College, Kollam, Kerala, India
bDepartment of Pharmaceutical Chemistry, College of Pharmacy, King Saud University,
Riyadh 11451, Saudi Arabia
cR and D, Bharathiar University, Coimbatore, Tamilnadu, India
dDepartment of Physics, IES College of Engineering, Chittilappilly, Thrissur, Kerala, India.
e University of Novi Sad, Faculty of Sciences, Department of Physics, Trg D. Obradovića 4,
21000 Novi Sad, Serbia
fUniversity of Novi Sad, Faculty of Sciences, Department of Chemistry, Biochemistry and
Environmental Protection, Trg D. Obradovića 3, 21000 Novi Sad, Serbia
gAnkara University Faculty of Pharmacy, Department of Pharmaceutical Chemistry, TR-
06100, Tandogan, Ankara, Turkey
hDepartment of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020,
Antwerp, Belgium
*author for correspondence: email: sypanicker@rediffmail.com
Abstract
Antimicrobial
active
5-[(4-nitrophenyl)acetamido]-2-(4-tert-butylphenyl)benzoxazole
(NATPB) was synthesized and observed IR, Raman bands are compared with the
theoretically predicted wave numbers. In the IR spectrum the NH stretching wave number
splits into a doublet with a noted difference and is red shifted from the computed value,
which indicates the weakening of NH bond resulting in proton transfer to the neighboring
oxygen atom. The HOMO-LUMO plots reveal the charge transfer in the molecular system
through the conjugated paths. The electrophilic and nucleophilic reactive sites are identified
from the MEP plot. Mapping of average local ionization energy (ALIE) values to the electron
density surface served us as a tool for prediction of molecule sites possibly prone to
electrophilic attacks. Other important reactive centres of the title molecule were detected by
calculations of Fukui functions. Calculations of bond dissociation energies (BDE) for
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hydrogen abstraction were used in order to assess whether the NATPB molecules is prone to
autoxidation mechanism or not, while BDE of the remaining single acyclic bonds were used
in order to determine the weakest bond. Interaction properties with water were investigated
by molecular dynamics (MD) simulations and calculations of radial distribution functions
(RDFs). The compound possessed broad spectrum activity against all of the tested Gram-
positive and Gram-negative bacteria and yeasts, their minimum inhibitory concentrations
(MICs) ranging between 32 - 128 µg/ml. The compound exhibited significant antibacterial
activity (32 µg/ml) against an antibiotic resistant E. faecalis isolate, at same potency with the
compared standard drugs vancomycin and gentamycin sulfate. The molecular docking studies
show that the compound might exhibit inhibitory activity against CDK inhibitors.
Keywords: DFT; benzoxazole; ALIE; RDF; BDE; Docking.
1.
Introduction
Benzoxazole contains a phenyl ring fused to an oxazole ring and this moiety has
found a number of practical applications and various biological activities and wide
therapeutical properties. Benzoxazole derivatives possess antibiotic [1], antibacterial [2],
antifungal [3,4] antitumor [5,6] anti-inflammatory [7], antiulcer [8] and anti-tubercular [9]
activities.
Organic molecules that are candidates for pharmaceutical formulations are synthetized to
be highly stable in aquatic surrounding. Unfortunately natural environmental conditions are
not suitable for their degradation in water [10-12] and this has already led to their presence
and accumulation in all types of waters all over the world [13]. Reactive and stability
properties of molecules dictate the fate of the pharmaceutical in the environment.
In general to improve the degradation techniques, forced degradation studies are
performed on the organic molecules that are candidates to be active components in
pharmaceuticals [14]. In this regard the advanced oxidation processes are of great importance
[13,15, 16]. However, these types of studies are very demanding from the aspect of needed
resources, thus the molecular modeling principles are used for rationalization and
optimization of such experiments. There are certain correlations between quantities that are
readily calculated by DFT calculations and MD simulations from one side and the
physicochemical properties of target molecules from the other. A fine example is
employment of DFT calculations of bond dissociation energies (BDE) that can be used for
the prediction of molecule sites where autoxidation mechanism might occur. Also, the
influence of water and possible hydrolysis of investigated molecules can be assessed by
molecular dynamics (MD) simulations and calculations of radial distribution functions.
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Taking into account the potential importance of the title molecule from the pharmaceutical
aspect, we have applied DFT calculations and MD simulations in order to predict some
important reactive properties. Obtained results are valuable for the future degradation studies
of the title compound.
2.
Experimental details
2.1
Materials and methods
The chemicals and solvents were purchased from Sigma-Aldrich (Munich, Germany)
and Fisher Scientific (Pittsburgh, PA, USA); they were used without purification. Silica gel
HF254 chromatoplates (0.3 mm) were used for thin layer chromatography, and the mobile
phase was chloroform/methanol (10:0.5). Melting point was recorded on a Stuart Scientific
SMP 1 instrument (Bibby Scientific Limited, Staffordshire, UK) and is uncorrected. NMR
spectra were recorded on a Varian Mercury 400 MHz NMR spectrometer (Palo Alto, CA,
USA). Trimethylsilane (TMS) was used as an internal standard. The mass spectra was
recorded on a Waters ZQ Micromass LC-MS spectrometer (Milford, MA, USA) using the
ESI(+) method.
The FT-IR (Fig. 1) and FT-Raman spectra (Fig. 2) were recorded using KBr pellets on
a DR/Jasco FT-IR 6300 spectrometer and on a Bruker RFS 100/s, Germany, with excitation
wavelength 1064 nm.
Materials used in the microbiology study were; Mueller Hinton agar (MHA) (Merck,
Darmstadt, Germany), Mueller Hinton broth (MHB) (Merck), Sabouraud dextrose agar
(SDA) (Merck), RPMI-1640 medium with L-glutamine (Sigma-Aldrich), 3-[N-morpholino]-
propane-sulfonic acid (MOPS) (Sigma-Aldrich), 96-well micro plates (BD, Franklin Lakes,
NJ, USA), ampicillin (Mustafa Nevzat Pharmaceuticals, Istanbul, Turkey), gentamycin
sulfate (Paninkret Chem.-Pharm., Pinneberg, Germany), ofloxacin (Zhejiang Huangyan East
Asia Chemical Co. Ltd., Huangyan, Zhejiang, China), vancomycin (Mayne Pharma,
Salisbury South, SA, Australia), meropenem (Astra Zeneca, Istanbul, Turkey), fluconazole
(Sigma-Aldrich), amphotericin B (Riedel de Haen, Seelze, Germany), isoniazid (Sigma-
Aldrich), ethambutol (Sigma-Aldrich), DMSO (Riedel de Haen).
Microorganisms used in the assay were; Klebsiella pneumoniae clinical isolate
(extended beta lactamase spectrum (ESBL)), Escherichia coli isolate (ESBL), Enterococcus
faecalis isolate (resistant to vancomycin (VRE)), and Staphylococcus aureus isolate (resistant
to methicilline (MRSA)), K. pneumoniae RSKK 574, E. coli ATCC 25922, E. faecalis
ATCC 29212, S. aureus ATCC 29213, Candida albicans ATCC 10231, Candida krusei
ATCC 6258, Mycobacterium tuberculosis H37RV ATCC 27294 and a clinical isolate of M.
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tuberculosis. Reference strains and clinical isolates were provided by Gazi University,
Faculty of Pharmacy, Department of Pharmaceutical Microbiology, Culture Collection,
Ankara, Turkey and Gazi University Hospital Microbiology Laboratory, Ankara, Turkey,
respectively.
2.2
Chemistry
General procedure for the preparation of 5-[(4-nitrophenyl)acetamido]-2-(4-
tertbutylphenyl)benzoxazole
Firstly, 5-amino-2-(4-tert-butylphenyl)-benzoxazole was synthesized by heating 0.02
mol 2,4-diaminophenol·2.HCl with 0.02mol 4-tert-butylbenzoic acid in 25 g polyphosphoric
acid (PPA) and stirring for 3-4 h. At the end of the reaction period, the residue was poured in
to an ice/water mixture and the solution was neutralized with 10% NaOH. The resulting
precipitate was filtered, washed with distilled water, dissolved in boiling ethanol with 0.2 g
charcoal, and filtered off. Then distilled water was added to the filtrate slowly in order to
stimulate crystallization. The crude compound 3 was obtained by filtering and drying the
crystalline material [17]. Then, 4-nitrophenylacetic acid (0.5 mmol) and thionylchloride (1.5
ml) were refluxed in benzene (5 ml) at 80°C for 3h. Excess thionylchloride was removed in
vacuo. The 4-nitrophenylacetic acid chloride (5) was dissolved in ether (10 ml) and this
solution added during 1 h to a stirred, ice-cold mixture of 5-amino-2-[4-tert-
butylphenyl]benzoxazole (3) (0.5mmol), sodiumbicarbonate (0.5 mmol), diethylether (10 ml)
and water (10 ml). The mixture was kept stirred overnight at room temperature and filtered.
The precipitate was washed with water, 2M HCl and water, respectively and finally with
ether to give compound. The product was re-crystallized from ethanol-water as needles which
are dried in vacuo. (Scheme 1).
2.3
Microbiological assays
For microbiological assays, standard powders of ampicillin, meropenem, gentamycin
sulfate, ofloxacin, vancomycin, fluconazole, amphotericin B, isoniazid, and ethambutol were
dissolved in appropriate solvents recommended by Clinical and Laboratory Standards
Institute (CLSI) guidelines [18, 19]. Stock solutions of the test compounds were prepared in
DMSO. Bacterial susceptibility testing was performed according to the guidelines of CLSI
M100-S18 [19]. MHB was added to each well of the micro plates. The bacterial suspensions
used for inoculation were prepared at 106 CFU/ml by diluting fresh cultures at McFarl and 0.5
density. Suspensions of the bacteria at 106 CFU/ml were inoculated to the two-fold diluted
solution of the compounds. A 10-µl bacterium inoculum was added to each well of the micro
plates. There were 105 CFU/ml bacteria in the wells after inoculations. Micro plates were
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incubated at 37°C overnight. Fungal susceptibility testing was performed according to the
guidelines of CLSI M27-A3 [18]. RPMI-1640 medium with L-glutamine buffered to pH 7
with MOPS was added to each well of the micro plates. The colonies were suspended in
sterile saline, and the resulting suspension was adjusted to McFarland 0.5 density. A working
suspension was prepared by appropriate dilution of the stock suspension. A 10-µl bacterium
inoculum was added to each well of the micro plates resulting in 103 CFU/ml yeasts in the
wells. Micro plates were incubated at 35 °C for 24-48 hours.
After incubation, the lowest concentration of the compounds that completely inhibited
macroscopic growth was determined and reported as minimum inhibitory concentration
(MIC). All solvents and diluents, pure microorganisms, and pure media were used in control
wells. All experiments were done in three parallel series. The data on the antimicrobial
activity of the compounds and the control drugs as MIC (µg/ml) values are given in Table 1.
The synthesized compounds were found to possess MIC values between 32 - 128 µg/ml for
some Mycobacterium tuberculosis, Gram-negative, Gram-positive bacteria and their isolates
and some fungi. The compound exhibited significant antibacterial activity (32 µg/ml) against
an antibiotic resistant E. faecalis isolate, at same potency with the compared standard drugs
vancomycin and gentamycin sulfate. Moreover, the synthesized compound exhibited the
same antifungal activity against C. krusei with MIC values of 64 µg/ml with the tested
reference drug fluconazole.
3.
Computational Details
Molecular geometries and vibrational wavenumbers of the title compound were
computed using B3LYP/6-311++G(d,p) (5D, 7F) [20]. The theoretically obtained
wavenumbers are scaled by using the scaling factor 0.9613 [21] for better agreement with the
experimental results and vibrational assignments are done with help of potential energy
distribution [22] and GaussView software [23]. The NMR chemical shifts were calculated
within the gauge-independent atomic orbital approach applying the same method used for
geometry optimization. NBO, MEP and frontier molecular orbital analysis were achieved
using B3LYP/6-311++G(d,p) (5D, 7F) basis set. The natural bond orbital (NBO) calculations
were performed using NBO 3.1 program [24] as implemented in the Gaussian09 package at
the DFT/B3LYP level. The optimized geometrical (Fig.3) parameters are given in table 2.
Jaguar 9.0 [25] and Desmond [26-29] programs, as implemented in Schrödinger Materials
Science Suite 2015-4, have been used for DFT calculations and MD simulations,
respectively, in order to gain additional insight into the local reactivity properties of the
NATPB molecule. With Jaguar ALIE, Fukui functions and BDE have been obtained using
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the B3LYP exchange-correlation functional [30], with 6-311++G(d,p), 6-31++G(d,p) and 6-
311G(d,p) basis sets, respectively. Based on the work of Johnson et al. [31, 32], which is
implemented in Jaguar program, noncovalent interactions have been investigated. MD
simulations have been performed with OPLS 2005 force field [33] and within NPT ensemble
class. The system was modeled by placing one NATPB molecule into the cubic box with
approximately 3000 water molecules and the simulation time was set to 10 ns. Cut off radius
was set to 12 Å, temperature to 300 K, while pressure was set to 1.0325 bar. Solvent was
treated within the simple point charge (SPC) model [34]. In all cases when Jaguar and
Desmond were used, input and output files were manipulated by Maestro graphical user
interface application for Schrödinger Materials Science Suite 2015-4.
4.
Results and Discussion
In the following discussion, the rings, C1-C2-C4-C8-C6-C3, C11-N22-C13-C12-O21, C12-C13-C15-
C18-C16-C14, and C30-C32-C36-C39-C35-C31 are designated as PhI, PhII, PhIII and PhIV,
respectively.
4.1
Geometrical parameters
The Phenyl ring C-C bond lengths of the title compound are, 1.4092-1.3876 Ǻ for
PhI, 1.4107-1.3811 Ǻ for PhIII and 1.4018-1.3887 Ǻ for PhIV rings which are in agreement
with reported literature [35]. In the present case, the C-N bonds lengths are, C11-N22 = 1.2990
Ǻ, C13-N22 = 1.3894 Ǻ, C18-N23 = 1.4188 Ǻ, C25-N23 = 1.3705 Ǻ and C39-N40 (nitro) = 1.4777
Ǻ. The C-O bond length of the title compound is, C=O = 1.2186 Ǻ and the reported values
are 1.2235 Ǻ [36] and 1.2253 Ǻ [36]. The C-O bond lengths of the title compound are, C11-
O21 = 1.3794 Ǻ and C12-O21 = 1.3713 Ǻ while the reported values for a similar derivative are
1.3871 Ǻ and 1.3653 Ǻ [37].
For the nitro group of the title compound, the N-O bond lengths are N40-O41 = 1.2248
Ǻ, N40-O42 = 1.2254 Ǻ, the C-C-N bond angle is 117.7° and O-N-O bond angle is 124.6°
while the reported values are 1.2236, 1.2257 Ǻ (N-O) and 117.3, 117.7° (CNO) [35].
At the position C1, the bond angles are, C2-C1-C3 = 117.1°, C2-C1-C43 = 122.9° and
C3-C1-C43 = 120.9° and the differences in the angles are due to the interaction between the
methyl groups and the ring PhI. The interactions between the phenyl rings, PhI and PhII are
revealed for the bond angles at C8 and C11 positions, which are respectively, C4-C8-C6 =
118.7°, C4-C8-C11 = 119.7°, C6-C8-C11 = 121.6° and O21-C11-N22 = 114.7°, O21-C11-C8 =
117.4°, N22-C11-C8 = 127.9°. The bond angles around C18 position are, C15-C18-C16 = 121.2°,
C15-C18-N23 = 116.5° and C16-C18-N23 = 122.3° and this asymmetry in angles is due to the
interaction between the ring PhIII and the NH group. The interaction between the carbonyl
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with group with the neighbouring moieties, NH and CH2 is given by the bond angles at the
position C25 and these angles are, N23-C25-C27 = 114.3°, N23-C25-O26 = 124.7°, and C27-C25-
O26 = 121.0°. At C39 position, the angle C35-C39-C36 is increased by 1.8°, C35-C39-N40 is
decreased by 0.8° and C36-C39-N40 is decreased by 1.0° from 120° and this is due to the
interaction between the nitro group and H37,38
4.2 IR and Raman spectra
The vibrational assignments of the title compound are given in Table 3. For the title
.
compound, the carbonyl stretching mode is assigned at 1672 cm-1 in the IR spectrum, 1680
cm-1 in the Raman spectrum, 1677 cm-1 theoretically while the C-O stretching modes are at
1175, 904 cm-1 theoretically and according to literature, the C=O stretching modes are
assigned in the range 1850-1550 cm-1 [38] and the C-O-C stretching modes are in the range
1200-900 cm-1 [39, 40]. For the C=O mode at 1677 cm-1 the IR intensity is 259.89 with bands
in the IR spectrum and with a PED of 75% and for the C-O modes at 1175 and 904 cm-1, the
PEDs are 43 and 47% with low IR intensities and no bands in the IR spectrum. Sebastian et
al. reported the carbonyl stretching mode at 1694 cm-1 (IR) 1696 cm-1 (Raman) and at 1699
cm-1 (DFT) [35]. For a similar derivative, the C-O-C stretching modes are reported at 1173,
890 cm-1 in the IR spectrum, 1174, 888 cm-1 in the Raman spectrum, 1172, 893 cm-1
theoretically by Parveen et al. [37].
NO2 stretching vibrations are expected in the regions 1565-1505 and 1375-1305 cm-1
according to literature [41] and for the title compound, these modes are assigned at 1514 cm-1
in the IR spectrum, 1512 cm-1 in the Raman spectrum and 1515, 1315 cm-1 theoretically with
high IR intensities and PEDs 75 and 55% [41]. Sebastian et al. [35] reported NO2 stretching
modes at 1566, 1345 cm-1 in the IR spectrum, 1565, 1345 cm-1 in the Raman spectrum and
1568, 1342 cm-1 theoretically. The deformation modes of NO2 are expected in the regions at
850 ± 60, 740 ± 50 and 540 ± 70 cm-1 according to literature [41] and in the present case,
bands observed at 842, 705, 468 cm-1 (IR), 702, 598, 460 cm-1 (Raman) and 840, 703, 602,
465 cm-1 (DFT) are assigned as NO2 deformation modes. The PEDs of these deformation
modes are in the range 33-47% with low values of IR intensity and Raman activities.NO2
deformation modes are reported at 811, 724, 526 cm-1 (IR), 810, 730, 530 cm-1 (Raman) and
808, 726, 528 cm-1 (DFT) [35].
According to literature, the NH stretching vibration is expected in the range 3500-
3300 cm-1 and the NH bending modes around 1500 and 1250 cm-1 [42, 43] and in the present
case, these modes are assigned at 3480, 3260 cm-1 (IR), 3480 cm-1 (Raman), 3485 cm-1 (DFT)
(stretching), 1500 cm-1 (Raman), 1506, 1214 cm-1 (DFT) (bending). These modes have PEDs
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of 100, 49 and 30%. These modes are reported at 3462, 3324 cm-1 (IR), 3450 cm-1 (Raman),
3400 cm-1 (DFT) (stretching), 1508, 1219 cm-1 (DFT) [35]. The NH stretching wavenumber
has two values in the IR spectrum with a difference of 220 cm-1 and is red shifted by 225 cm-1
from the computed value, which indicates the weakening of NH bond resulting in proton
transfer to the neighbouring oxygen atom. Mary et al. reported values of NH modes at 1587,
1250, 650 cm-1 (IR), 1580, 1277, 652 cm-1 (DFT) [44]. In the present case, the NH out-of-
plane mode is assigned at 522 cm-1 theoretically [41-43].
The CN stretching modes are expected in the region 1100-1300 cm-1 [39] and in the
present case the bands at 1230, 1142 cm-1 in the IR spectrum, 1230, 1143 cm-1 in the Raman
spectrum, 1255, 1232, 1139 cm-1 theoretically are assigned as these modes which are in
agreement with literature [45]. Aromatic nitro compounds show a C-N stretching vibration
near [39] 870 cm-1. The band at 900 cm-1 theoretically is assigned as the C-N stretching mode
of nitro group attached with the phenyl ring of the title compound. In the present case all the
C-N stretching modes have PEDs around 40%. The C-N stretching modes are reported at
1258, 1245, 1103, 897 cm-1 (DFT) [46], 1215 cm-1 (DFT) [47]. The C=N stretching mode of
the title compound is observed at 1526 cm-1 in the Raman spectrum and at 1525 cm-1
theoretically as expected [39].
The methyl stretching modes of the title compound are observed at 2964, 2902 cm-1 in
the IR spectrum, 2982, 2963, 2916, 2901 cm-1 in the Raman spectrum and in the range 2979-
2905 cm-1 theoretically as expected [41, 42]. The bending modes of the methyl groups are
observed at 1427, 1340 cm-1 in the IR spectrum, 1451, 1428, 1342, 1321, 1085, 1007, 891
cm-1 in the Raman and in the range 1463-890 cm-1 theoretically [41, 42].
The CC3 stretching modes are expected in the ranges 1295-1175 cm-1 and 890-710
cm-1 [41, 42] and in the present case these modes are assigned at 806 cm-1 in the IR spectrum,
1236, 808 cm-1 in the Raman spectrum and at 1234, 1173, 805 cm-1 theoretically with PEDs
around 44-49%. Joseph et al. reported the CC3 stretching modes at 1244, 907 cm-1 in the IR
spectrum, 1247 cm-1 in Raman spectrum and at 1286, 1249, 906 cm-1 theoretically [48].
Joseph et al. reported the CC3 stretching modes at 1244, 907 cm-1 in the IR spectrum, 1247
cm-1 in Raman spectrum and at 1286, 1249, 906 cm-1 theoretically [48]. The deformation
modes of the CC3 group are expected in the regions, 435± 85, 335 ± 80 and 300 ± 80 cm-1
(total five modes, two asymmetric, one symmetric and two rocking) and for the title
compound, these deformation modes are assigned at 446, 395, 341, 320 and 279 cm-1
theoretically and the reported values are 496, 326, 313, 290, 219 cm-1 theoretically [48]. The
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CC3 deformation modes have PEDs less than 50% except for the mode at 320 cm-1 has a high
PED of 60%.
The CH2 modes of the title compound are observed at 1265 cm-1 in the IR spectrum,
2965, 2932, 1419, 1264 cm-1 in the Raman spectrum experimentally and the PED analysis
gives these modes at 2966, 2929 cm-1 (stretching) and 1434, 1422, 1263, 1214 cm-1
(deformation modes) which are in agreement with the literature [41, 42].
The phenyl CH stretching modes of the title compound are assigned at 3082 cm-1
(IR), 3077 cm-1 (Raman), 3085, 3076, 3068, 3052 cm-1 (DFT) for PhI, 3115 cm-1 (IR) 3122
cm-1 (Raman), 3121, 3077, 3052 cm-1 (DFT) for PhIII and 3044 cm-1 (IR), 3097, 3077, 3030
cm-1 (Raman), 3098, 3098, 3076, 3049 cm-1 (DFT) for PhIV rings as expected [41]. In the
present case, the phenyl ring CC stretching modes are assigned at 1550, 1473 cm-1 (IR),
1550, 1470, 1385 cm-1 (Raman), 1588, 1545, 1473, 1383, 1280 cm-1 (DFT), for PhI, 1601,
1402 cm-1 (IR), 1321 cm-1 (Raman), 1599 1583, 1437, 1396, 1323 cm-1 (DFT ) for PhIII and
1575 cm-1 (Raman), 1580, 1573, 1464, 1391, 1306 cm-1 (DFT) for PhIV as expected [41].
Tri-substituted phenyl rings have three wavenumber intervals for the ring breathing mode:
500-660, 1050-1100 and 600-750 cm-1 for light substituent, heavy substituent and mixed
substituent according to literature [49]. For the title compound, the ring breathing mode of tri-
substituted benzene ring is assigned at 1101 cm-1 theoretically with a PED of 46%. The ring
breathing mode of tri-substituted phenyl rings are reported at 1110, 1129 cm-1 [50] and at
1109 cm-1 in the IR spectrum, 1100 cm-1 theoretically 1109 cm-1 (IR), 1100 cm-1 (DFT) [51].
The ring breathing mode of para-substituted phenyl rings with entirely different
substituent are expected in the range 780-880 cm-1 according to literature [49] and in the
present case, this is confirmed by the bands at 815 cm-1 and 781 cm-1 by PED analysis and
the PED values are 47 and 52%. The phenyl ring breathing mode of para-substituted phenyl
rings was reported at 795 cm-1 [52], at 873 cm-1 in the IR spectrum and at 861 cm-1
theoretically [53] and at 753 cm-1 in IR spectrum, 793, 759 cm-1 theoretically [54].
The in-plane and out-of-plane CH bending vibrations of phenyl rings are expected
above and below 1000 cm-1 [41] and for the title compound, these modes are assigned at
1292, 1185 cm-1 (IR), 1293 cm-1 (Raman), 1295, 1178, 1163, 1078 cm-1 (DFT) for PhI, 1105,
1142 cm-1 (IR), 1105, 1143 cm-1 (Raman), 1258, 1139, 1103 cm-1 (DFT) for PhIII, 1170,
1068 cm-1 (IR), 1068 cm-1 (Raman), 1288, 1168, 1158, 1074 cm-1 (DFT) for PhIV (in-plane
CH deformation modes) and at 952 cm-1 (IR), 954, 944, 829, 819 cm-1 (DFT) for PhI, 930
cm-1 (IR), 930 cm-1 (Raman), 928, 823, 801 cm-1 (DFT) for PhIII, 970, 842 cm-1 (IR), 970
cm-1 (Raman), 965, 956, 840, 818 cm-1 (DFT) for PhIV (out-of-plane deformation modes).
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4.3
NMR spectra
1
GIAO H- and 13C-NMR chemical shifts with respect to trimethylsilane were
calculated using the DFT/B3LYP method (Table 4). The predicted chemical shifts of
aromatic protons of the title compound are in the range 7.851-8.872 for PhI, 7.0809-9.1635
for PhIII and 7.6067-8.7193 for PhIV. The experimental shifts are 7.62-7.65 for PhI, 7.53-
8.14 for PhIII and 8.10-8.24 for PhIV. For the tert-butyl group, the proton shifts are in the
range, 1.6335-2.7547 (predicted), 1.33 (experimental) while in methylene group the shifts are
4.2892, 3.3271 (predicted), 3.89 (experimental). The hydrogen atom of amide group in this
compound appears at a higher chemical shift of 6.5392 ppm theoretically, while the
experimental shift is 10.49. We noted that, δcalc of the NH protons strongly deviate from the
experimental data due to the high polarity of these bonds.
13
For organic molecules, the range for C NMR chemical shift is usually greater than
100 ppm [55]. For the carbonyl group, the carbon atom has a low lying excited state
involving the movement of electrons from the oxygen lone pair to anti-bonding π orbital that
generates a paramagnetic current [56] and this n→π* transition produces a large shift to a
higher frequency and hence the carbonyl carbon signals have a weaker intensity and appear in
the range, 150-220 ppm [58, 58]. Thus it easy to recognize the carbonyl absorptions from the
other resonances and for the title compound carbonyl sift is 162.738. The aromatic carbons
give resonance in overlapped areas of NMR spectrum with chemical shift values from 100 to
150 ppm [59] and in the present case, the chemical shifts of the aromatic carbon atoms are,
125.4344-153.0048 PhI, 108.5366-147.2081 for PhIII and 124.2802-148.02324 for PhIV.
The chemical shifts of the other carbon atoms are 53.1382 (C27), 163.456 (C11), 44.009
(C43), 38.7995 (C44), 38.7946 (C48) and 35.2413 (C52).
4.4
Nonlinear Optical properties
For the title compound, the polarizability is 5.5574×10-23 esu and the first and second
hyperpolarizabilities are 211.26×10-30 and -85.049×10-37 esu. The first hyperpolarizability of
the title compound is 1625 times that of the standard NLO material urea [60] and the reported
first and second hyperpolarizability of a similar derivative are 31.139×10-30 and -22.127×10-
37
esu [61]. The high values of hyperpolarizability may be due to the electron cloud transfer
from donor to acceptor which makes the system highly polarized and the charge transfer.
4.5
Frontier Molecular Orbital
The intra molecular charge transfer between donor and acceptor groups through the
conjugated paths can be explained by frontier molecular orbital analysis [62]. In the present
case the HOMO and LUMO energies are -8.168 and -5.280 eV, respectively. The ionization
10

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energy I = -EHOMO = 8.168 eV and electron affinity A = -ELUMO = 5.280 eV and energy gap =
2.888 eV. The global chemical descriptors are given as hardness η = (I-A)/2, chemical
potential µ = -(I+A)/2 and electronegativity index ω =µ2/2η [63, 64]. In the present case η, µ
and ω are 1.444, -6.724 and 15.66 eV respectively. In the HOMO-LUMO plot (Fig. 4), the
HOMO is localized over the acetamido group, benzoxazole, trisubstituted phenyl ring and the
phenyl ring attached with the tert-butyl group, while the LUMO is over the tert-butyl phenyl,
ring, butyl group, benzoxazole ring and trisubstituted phenyl ring and there is a charge
transfer in the molecular system through the conjugated paths.
4.6
Molecular Electrostatic Potential
Molecular electrostatic potential of the title compound is calculated to predict the
reactive sites of electrophilic and nucleophilic attacks. In the MEP map red represents most
negative region, blue represents most positive region and green represents zero potential. The
negative, red and yellow regions in the MEP plot were related to electrophilic reactivity and
positive, blue region to nucleophilic reactivity. From the MEP plot (Fig. 5) it is clear that the
nitro group, carbonyl oxygen atom and nitrogen atom in the benzoxazole ring are the most
negative regions and nitrogen atom in the NH moiety is the most positive region.
4.7
ALIE surface, Fukui functions and non-covalent interactions
Determination of molecule sites prone to electrophilic attacks is of great importance
for the overall understanding of the reactivity of some molecule. In this regards very
frequently MEP surfaces are employed, while ALIE surfaces provide even more useful
results concerning this. Namely, ALIE was introduced by Sjoberg et al. [65, 66] to indicate
molecule areas where electrons are least tightly bound. It is defined as a sum of orbital
energies weighted by the orbital densities:
r
ρi
(
r
)
εi
)
I
(
r =
)
,
(1)
r
∑
ρ
(
r
i
r
r
ρi
(
r
)
ε
r
,
i
where
represents the electronic density of the i-th molecular orbital at the point
r
ρ
(
r
)
represents the orbital energy and
is the total electronic density function. In this work
ALIE values were visualized by their mapping to the electron density surface, Fig.6
Results concerning the ALIE surface of NATPB molecule indicate that two benzene
rings and nitrogen atom N22 are possibly prone to electrophilic attacks. Namely, at these
locations the red colour indicates molecule sites where electrons are least tightly bound and
where they are most easily removed. On the other side the blue colour indicates molecule
locations where electrons are most tightly bound and the most important locations from this
11

ACCEPTED MANUSCRIPT
aspect are in the near vicinity of one benzene ring, oxygen atom O42 and hydrogen atom
H24. Fig.6 also has visualized two intra-molecular non-covalent interactions involving atoms
H20, H33 and O26.
In the same time it is also useful to track the changes of molecule’s electron density with
the addition or removal of charge. This can be done by the calculations of Fukui functions
and in such way one is able to detect possible important reactive properties when molecule
acts as electrophile or nucleophile. In Jaguar program a finite difference approximation is
used for the calculations of Fukui functions according to the following equations:
δ
(
ρ N +
(
r
)
−
ρ N
(
r
)
)
f + =
f − =
,
,
(2)
(3)
δ
δ
(
ρ N −
(
r
)
δ
−
ρ N
(
r
))
where N represents the number of electrons in reference state of the molecule, while
δ
is
fraction of electron which default value is set to be 0.01 [67].
In this case also, the values of Fukui functions have been mapped to the electron
+
density surface and the results are presented in Fig.7. Concerning the Fukui f function,
purple colour in Fig.7a is designating molecule areas where electron density increased after
the addition of charge. It can be seen that when molecule acts as an electrophile electron
density increases in the near vicinity of NO2 designating this part of the molecule as an
important reactive centre. On the other side concerning the Fukui f – function red colour in
Fig.7b is designating molecule areas where electron density decreases after the removal of
charge, thus it can be concluded that when molecule acts as a nucleophile electron density
decreases in the near vicinity of carbon atom C27.
4.8
Natural Bond Orbital Analysis
The strong inter molecular hyper conjugative interactions (Tables 5 and 6) in the
molecular system are listed below: C11-N22 from O21 of n2(O21)→π*(C11-N22) which
increases the electron density as, 0.31245e that weakens the respective bonds C11-N22 leading
to stabilization of 34.63 kJ/mol; C25-O26 from N23of n1(N23)→π*(C25-O26) which increases
the electron density as, 0.28955e that weakens the respective bonds C25-O26 leading to
stabilization of 63.10 kJ/mol; N23-C25 from O26 of n2(O26)→σ*(N23-C25) which increases the
electron density as, 0.07566e that weakens the respective bonds N23-C25 leading to
stabilization of 26.23 kJ/mol; N40-O41 from O42 of n3(O42)→π*(N40-O41) which increases the
electron density as, 0.62292e that weakens the respective bonds N40-O41 leading to
stabilization of 164.96 kJ/mol; N40-O42 from O42 of n2(O41)→σ*(N40-O42) which increases
12

ACCEPTED MANUSCRIPT
the electron density as, 0.05655e which weakens respective bond N40-O42 leading to
stabilization of 19.44kJ/mol. The important bonding in terms of the natural hybrid orbital are,
n2(O21), n2(O26), n2(O41) and n3(O42) with higher energies, -0.33848, -0.25665, -0.28803, -
0.27160a.u, considerable p-characters (100%), and low occupation numbers, 1.73156,
1.85607, 1.89690, 1.44578; while the orbital, n1(O21), n1(O26), n1(O41), n1(O42) occupy lower
energies, -0.59151, -0.68247, -0.79162, -0.79187a.u, with p-characters, 62.33, 42.08, 25.55,
25.53% and high occupation number, 1.96933, 1.97337, 1.98105, 1.98102. Thus, a very
close to pure p-type lone pair orbital participates in the electron donation to the π*(C11-N22)
orbital for n2(O21)→π*(C11-N22), σ*(N23-C25) orbital for n2(O26)→σ*(N23-C25), σ*(N40-O42)
orbital for n2(O41)→σ*(N40-O42), π*(N40-O41) orbital for n3(O42)→π*(N40-O41),π*(C25-
O26)orbital for n1(n23)→π*(C25-O26).
4.9
Reactive and degradation properties based on autoxidation and hydrolysis
Local reactivity properties of important biologically active molecules can be
investigated and in such a way forced degradation experiments can be significantly
rationalized [68] by using DFT calculations and MD simulations. Concerning the DFT
calculations, if the BDE for hydrogen abstraction has appropriate value then it can be a
candidate for the starting point in the case of autoxidation mechanism. In this regard it is
important to mention that all peroxy radicals have similar BDE values (87–92 kcal/mol) and
it can be approximated that they are independent on the chemical surrounding [69, 70].
On the other side the study of Wright et al. [71] indicated that the possibility for
autoxidation mechanism is the highest if the BDE values for the hydrogen abstraction are in
the interval of 75 to 85kcal/mol. Therefore, in order to investigate the possibility for
autoxidation of NATPB molecule we have calculated BDE values for hydrogen abstraction.
Also, BDE values of the remaining single acyclic bonds have been calculated to determine
the weakest bonds and therefore possible locations where degradation process could start,
Fig.8.
According to the results presented in Fig.8 there is one BDE value for hydrogen abstraction
which could be considered as interesting for the autoxidation mechanism. Namely, the BDE
value for the abstraction of hydrogen atom H28, denoted with number 7, is equal to ~88
kcal/mol. Of the remaining single acyclic bonds the lowest BDE values have been obtained
for the ones denoted with numbers 14 and 15. These results indicate that the mentioned bonds
are the weakest and that degradation process could start by detaching of part of the molecule
with benzene ring and NO2 group from one side, while from the other side degradation could
start by detaching of the methyl group. The fact that the lowest BDE value for hydrogen
13

ACCEPTED MANUSCRIPT
abstraction is very close to the weakest bond is very important, since it indicates that
oxidation could have important role in the degradation of the NATPB molecule.
Atoms of NATPB molecule with relatively significant interactions with water
molecules have been determined by calculations of RDF after MD simulations. RDF, g(r),
gives the probability of finding a particle in the distance r from another particle [72] and
representative g(r) curves are provided in Fig.9.
RDF results presented in Fig.9 indicate that five carbon and three non-carbon atoms
of NATPB molecule have relatively pronounced interactions with water molecules. Of
carbon atoms the most important is the carbon atom C43, with maximal g(r) value of around
1.6 and with peak distance located at around 4.75 Å. The peak distance of carbon atom C30 is
located in similar location as in the case of C43, but its maximal g(r) value is much lower,
around 1.2. Carbon atoms C6 and C25 have significantly lower maximal g(r) values than
C43, but their peak distances are located at much shorter distances, around 3.5 Å. Of non-
carbon atoms the RDF that indicates the most pronounced interactions with water molecules
is the RDF of hydrogen atom H24 with maximal g(r) value of around 0.9, but located at
distance lower than 2 Å. Oxygen atom O26 has similar maximal g(r) value, but its located at
distance somewhat higher than 3.5 Å. Nitrogen atom N40 also has the highest maximal g(r)
value of non-carbon atoms, located at distance of around 4 Å. RDF results related to atom
O26 indicate that autoxidation and hydrolysis mechanisms could compete, since the
mentioned atom is close to the hydrogen atoms for which abstraction BDE values are the
lowest. In the same time O26 is practically adjacent bond to the weakest bond according to
the BDE results, meaning that hydrolysis could be important for the degradation properties of
this molecule. In the same time, beside Fukui functions RDFs also indicate the importance of
NO2 group for the general reactivity of NATPB molecule, as in Fig.9 it can be seen that
nitrogen atom N40 has pronounced interactions with water.
4.10 Molecular docking
Benzoxazoles are the structural isosteres of natural nucleotides and interact easily
with the biopolymers that they constitute an important class of heterocyclic compounds with
antimicrobial, antitubercular, antiviral and antitumor [73] activity. Kumar et al. report the
activity of UK-1 (structurally unique bis(benzoxazole) natural product isolated from a strain
of Streptomyces) against a wide range of human cancer cell lines [74]. UK-1 displays a wide
spectrum of potent anticancer activity21 against leukemia, lymphoma and certain solid
tumour-derived cell lines [75]. Thus we simulate the title compound with CDK inhibitor as
anti-cancer. High resolution crystal structure of CDK inhibitors as anti-cancer was obtained
14

ACCEPTED MANUSCRIPT
from the protein data bank website (PDB ID: 2XMY) and all molecular docking calculations
were performed on Auto Dock-Vina software [76] and as reported in literature [52, 61]. The
ligand binds well at the active site was analyzed for detailed interactions (Figs. 10 and 11) in
Discovery Studio Visualizer 4.0 software [77]. The interactions obtained are: Amino acid
Lys88 forms π-cation, π-sigma and π-alkyl interaction with benzoxazole ring. Lys129, Lys88
shows H-bond interaction with NO2, C=O group respectively. Asp92 forms π-cation
interaction with phenyl ring and Ala95 forms alkyl interaction with CH3 group. The docked
ligand forms a stable complex with CDK inhibitors and gives a binding affinity value of -
8.3kcal/mol (table 7) and the compound might exhibit inhibitory activity against CDK
inhibitors.
5.
Conclusions
The FT-IR and FT-Raman studies of the title compound in the ground state were reported
experimentally and theoretically. Potential energy distribution of normal modes of vibrations
was done using GAR2PED program. The theoretically predicted geometrical parameters are
in agreement with that of similar derivatives. The title compound exhibited significant
antibacterial activity against an antibiotic resistant E. faecalis isolate and antifungal activity
against C. krusei. The first hyperpolarizability of the title compound is very much greater
than that of the standard NLO material urea and the high values of hyperpolarizability may be
due to the electron cloud transfer from donor to acceptor which makes the system highly
polarized and the charge transfer. MEP studies reveals that the nitro group, carbonyl oxygen
atom and nitrogen atom in the benzoxazole ring are the most negative regions and nitrogen
atom in the NH moiety is the most positive region. Two benzene rings and nitrogen atom
N22 have been recognized as possible molecule sites prone to electrophilic attacks.
Additionally, according to the Fukui functions NO2 group has been also recognized as
possibly important reactivity centre. Analysis of non-covalent interactions indicated that two
such interactions occurred within the NATPB molecule. BDE values indicate that there is one
hydrogen atom for whose abstraction less than 92 kcal/mol is necessary. In the same time
autoxidation mechanism could compete with hydrolysis, as in the close vicinity of the
mentioned hydrogen atom is oxygen atom O26 with significant interactions with water
molecule. The title compound forms stable complex with CDK inhibitors and exhibit
inhibitory activity against CDK inhibitors.
Acknowledgments
The authors would like to extend their appreciation to the Deanship of Scientific Research at
King Saud University for funding this study through the research group project No. RGP-
15

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1435-067. The authors are thankful to University of Antwerp for access to the University’s
CalcUA supercomputer cluster and the support received from Schrödinger Inc.
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Figure captions
Fig.1 FT-IR spectrum of 5-[(4-nitrophenyl)acetamido]-2-(4-tert-butylphenyl)benzoxazole
Fig.2 FT-Raman spectrum of 5-[(4-nitrophenyl)acetamido]-2-(4-tert-
butylphenyl)benzoxazole
Fig.3 Optimized geometry of 5-[(4-nitrophenyl)acetamido]-2-(4-tert-
butylphenyl)benzoxazole
Fig.4 HOMO-LUMO plots of 5-[(4-nitrophenyl)acetamido]-2-(4-tert-butylphenyl)
benzoxazole
Fig.5 MEP plot of 5-[(4-nitrophenyl)acetamido]-2-(4-tert-butylphenyl)benzoxazole
Fig.6 ALIE surface of 5-[(4-nitrophenyl)acetamido]-2-(4-tert-butylphenyl)benzoxazole
molecule
Fig.7 Fukui functions a) f + and b) f – of 5-[(4-nitrophenyl)acetamido]-2-(4-tert-butylphenyl)
benzoxazole molecule, Purple colour is positive colour, while red colour is the negative one
Fig.8 BDEs of all single acyclic bonds of 5-[(4-nitrophenyl)acetamido]-2-(4-tert-butylphenyl)
benzoxazole molecule
Fig.9 RDFs of atoms of 5-[(4-nitrophenyl)acetamido]-2-(4-tert-butylphenyl)benzoxazole with
pronounced interactions with: a) carbon atoms and b) non-carbon atoms
23

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Fig.10 Schematic for the docked conformation of active site of title compound at CDK
inhibitors
Fig.11 The docked protocol reproduced the co-crystallized conformation with H-bond
(green), p-cation (brown), p-sigma (violet), alkyl (pink) and H-bond receptor surface shown
24

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Table 1
Antimicrobial and antitubercular activity (MIC µg/ml) of synthesized compound 6 and the standard drugs
Microorganisma
-
E.c.
E.c.*
32
K.p. K.p.*
64 64
n.d. n.d.
S.a. S.a.* E.f.
128 128 64
E.f.* C.a. C.k. M.t. M.t.*
Compound 64
Vancomycin n.d.b
Gentamycin
32
32
64
64
32
32
n.d.
1
1
1
n.d. n.d. n.d. n.d.
sulfate
1
1024
<0.0625
64
0.5
256
0.125 32
0.125 -
4
2
1
32
0.5
4
n.d. n.d. n.d. n.d.
n.d. n.d. n.d. n.d.
n.d. n.d. n.d. n.d.
n.d. n.d. n.d. n.d.
Meropenem 0.0625
0.03 <0.0625
0.125 0.5
Ofloxacin
Ampicillin
<-.625
2
0.125 0.25
>2048
n.d.
2
>2048
0.5
>2048 1
0.5
Amphotericin B n.d.
Fluconzaloe n.d
n.d. n.d.
n.d. n.d.
n.d. n.d.
n.d. n.d.
n.d. n.d. n.d. n.d. 0.25
n.d. n.d. n.d. n.d.
2
n.d. n.d.
n.d. n.d.
n.d.
1
64
Isoniazid
n.d.
n.d.
n.d. n.d. n.d. n.d. n.d. n.d. <0.25 <0.25
n.d. n.d. n.d. n.d. n.d. n.d.
Ethambutol n.d.
n.d.
2
2
aE.c., Escherichia coli ATCC 25922; E.c.*,Escherichia coli isolate (ESBL); K.p., Klebsiella pneumoniae RSKK 574; K.p.*,
Klebsiella pneumoniae isolate (ESBL); S.a.,Staphylococcus aureus ATCC 29213; S.a.*, Staphylococcus aureus isolate (MRSA); E.f.,
Enterococcus faecalis ATCC 29212; E.f.*: Enterococcus faecalis isolate (VRE); C.a.,Candida albicans ATCC 10231;C.k., Candida
krusei ATCC 6258; M.t., Mycobacterium tuberculosis H37RV ATCC 27294; M.t.*, Mycobacterium tuberculosis isolate.
1

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bn.d., not determined (microbiological assays were not performed due to following reasons: antibacterial drugs were not assayed
against fungi and M. tuberculosis; antifungal drugs were not assayed against bacteria and M. tuberculosis; antitubercular drugs were
not assayed against bacteria and fungi; Gram-negative bacteria employed in the study are naturally resistant to vancomycin).
2

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Table 2
Geometrical parameters of the title compound
Bond lengths (Ǻ)
C1-C2
1.4015
1.3905
1.0836
1.402
C1-C3
1.4042
1.0817
1.3991
1.0828
1.299
C1-C43
1.5376
1.3876
1.083
C2-C4
C2-H5
C3-C6
C3-H7
C4-C8
C4-H9
C6-C8
C6-H10
C11-N22
C12-O21
C14-C16
C15-H19
C18-N23
C25-O26
C27-H29
C30-C32
C32-H34
C35-C39
C39-N40
C43-C44
C44-H45
C48-H49
C52-H53
C8-C11
1.4565
1.3983
1.3914
1.0824
1.4107
1.0083
1.5365
1.5154
1.0827
1.3907
1.0812
1.2248
1.5472
1.0942
1.0924
1.0934
C11-O21
C12-C14
C13-N22
C15-C18
C16-H20
N23-C25
C27-H28
C30-C31
C31-C35
C35-H37
C36-C39
N40-O42
C43-C52
C44-H47
C48-H51
C52-H55
1.3794
1.3811
1.3894
1.3998
1.0784
1.3705
1.0936
1.4018
1.3887
1.0813
1.3897
1.2254
1.5396
1.0934
1.0935
1.0934
C12-C13
C13-C15
C14-H17
C16-C18
N23-H24
C25-C27
C27-C30
C31-H33
C32-C36
C36-H38
N40-O41
C43-C48
C44-H46
C48-H50
C52-H54
1.3713
1.3951
1.0845
1.4188
1.2186
1.0925
1.3993
1.0846
1.392
1.4777
1.5469
1.0924
1.0942
1.0932
Bond angles (°)
C2-C1-C3
C1-C2-C4
C1-C3-C6
C2-C4-C8
C3-C6-C8
C4-C8-C6
C8-C11-O21
117.1 C2-C1-C43
121.7 C1-C2-H5
121.9 C1-C3-H7
120.4 C2-C4-H9
120.2 C3-C6-H10
118.7 C4-C8-C11
117.4 C8-C11-N22
122.9 C3-C1-C43
120.2 C4-C2-H5
119.9 C6-C3-H7
120.4 C8-C4-H9
120.0 C8-C6-H10
119.7 C6-C8-C11
127.9 O21-C11-N22
120.0
118.1
118.2
119.1
119.8
121.6 \
114.7
1

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C13-C12-C14
C12-C13-C15
C12-C14-C16
C13-C15-C18
C14-C16-C18
C15-C18-C16
C11-O21-C12
C18-N23-C25
N23-C25-C27
C25-C27-H29
H28-C27-C30
C27-C30-C32
C30-C31-C35
C30-C32-C36
C31-C35-C39
C32-C36-C39
C35-C39-N40
C39-N40-O42
C1-C43-C48
123.2 C13-C12-O21
107.4 C14-C12-O21
108.8 C15-C13-N22
122.2 C16-C14-H17
120.5 C18-C15-H19
120.2 C18-C16-H20
116.5 C16-C18-N23
104.8 C18-N23-H24
116.0 N23-C25-O26
121.0 C25-C27-H28
112.2 H28-C27-H29
109.8 C27-C30-C31
119.0 C30-C31-H33
119.9 C30-C32-H34
119.1 C31-C35-H37
119.7 C32-C36-H38
119.8 C35-C39-C36
119.0 C39-N40-O41
124.6 C1-C43-C44
112.4 C44-C43-C48
108.2 C43-C44-H45
110.9 H45-C44-H46
108.1 C43-C48-H49
110.9 H49-C48-H50
107.8 C43-C52-H53
111.9 H53-C52-H54
108.3
129.4
131.2
120.9
121.7
119.0
122.3
114.5
124.7
105.8
107.4
120.6
119.4
119.9
121.5
121.7
121.8
117.7
109.4
109.4
112.0
107.7
110.2
107.8
109.5
107.5
120.0 C12-C13-N22
116.9 C12-C14-H17
117.8 C13-C15-H19
120.9 C14-C16-H20
121.2 C15-C18-N23
104.3 C11-N22-C13
129.5 H24-N23-C25
114.3 O26-C25-C27
111.7 C25-C27-C30
109.7 H29-C27-C30
120.4 C31-C30-C32
120.7 H33-C31-C35
121.1 H34-C32-C36
118.9 H37-C35-C39
118.6 H38-C36-C39
119.2 C36-C39-N40
117.7 O41-N40-O42
109.3 C1-C43-C52
108.1 C48-C43-C52
110.1 C43-C44-H47
107.8 H46-C44-H47
111.9 C43-C48-H51
108.1 H50-C48-H51
112.0 C43-C52-H55
107.5 H54-C52-H55
C44-C43-C52
C43-C44-H46
H45-C44-H47
C43-C48-H50
H49-C48-H51
C43-C52-H54
H53-C52-H55
Dihedral angles (°)
C3-C1-C2-C4
C43-C1-C2-H5
C43-C1-C3-C6
C2-C1-C43-C48
-0.0 C3-C1-C2-H5
-0.2 C2-C1-C3-C6
-180.0 C43-C1-C3-H7
-119.4 C2-C1-C43-C52
179.9 C43-C1-C2-C4
-0.1 C2-C1-C3-H7
179.9
179.9
120.8
-59.3
0.0
0.7
C2-C1-C43-C44
C3-C1-C43-C44
2