A family of silatrane-armed triazole-encapped salicylaldehyde-derived Schiff bases: Synthesis, spectral analysis, and antimicrobial and quantum chemical evaluation

Article abstract of DOI:10.1002/aoc.3728

This work describes the successful synthesis of salicylaldehyde-derived Schiff base-linked organosilicon compounds following a highly efficient click approach. Hydroxyl-terminated Schiff bases were alkylated to bis-acetylenes (1–3) which upon 3?+?2 cycloaddition with 3-azidopropyltriethoxysilane yielded triazole-decorated bis-silanes (4–6). These silanes further underwent base-catalyzed transesterification to afford Schiff base-linked triazole-bound organosilatranes (7–9). The final silatranes as well as precursor alkynes and silanes were comprehensively characterized using NMR (¹H and ¹³C) and infrared spectroscopic techniques together with elemental analysis and mass spectrometry of compounds 7–9. Also, the structures of alkynes 1–3 and silatrane 7 were validated using single-crystal X-ray crystallography. Organosilatranes were initially screened for their pharmacokinetic profile using absorption, distribution, metabolism, excretion and toxicity (ADMET) tools and then explored for their antimicrobial activities, with compound 9 emerging as the most potent antimicrobial agent. Compounds 1–3 and 7–9 also underwent thorough computational analysis by applying the density functional theory (DFT) approach with B3LYP/6-31G(d) level of theory and the results were found to be consistent with the experimental data. Several DFT-based descriptors were also evaluated providing a valuable insight into molecular stability and reactivity.

Full text of DOI:10.1002/aoc.3728

Received: 21 September 2016
DOI 10.1002/aoc.3728
Revised: 30 November 2016
Accepted: 3 December 2016
F U L L PA P E R
A family of silatrane‐armed triazole‐encapped salicylaldehyde‐
derived Schiff bases: Synthesis, spectral analysis, and
antimicrobial and quantum chemical evaluation
1
1
1
1
2
Gurjaspreet Singh | Aanchal Arora | Sunita Rani | Pooja Kalra | Darpandeep Aulakh |
2
Mario Wriedt
1
Department of Chemistry and Centre of
This work describes the successful synthesis of salicylaldehyde‐derived Schiff base‐
linked organosilicon compounds following a highly efficient click approach.
Hydroxyl‐terminated Schiff bases were alkylated to bis‐acetylenes (1–3) which upon
Advanced Studies, Panjab University, Chandigarh,
1
60014, India
2
Functional Materials Design and X‐ray
Diffraction Lab, Department of Chemistry and
3
+ 2 cycloaddition with 3‐azidopropyltriethoxysilane yielded triazole‐decorated
Biomolecular Science, Clarkson University, Box
bis‐silanes (4–6). These silanes further underwent base‐catalyzed transesterification
to afford Schiff base‐linked triazole‐bound organosilatranes (7–9). The final
silatranes as well as precursor alkynes and silanes were comprehensively character-
5
810, Potsdam, New York 13699, U.S.A.
Correspondence
Gurjaspreet Singh, Department of Chemistry and
Centre of Advanced Studies, Panjab University,
Chandigarh, India.
1
13
ized using NMR ( H and C) and infrared spectroscopic techniques together with
elemental analysis and mass spectrometry of compounds 7–9. Also, the structures
of alkynes 1–3 and silatrane 7 were validated using single‐crystal X‐ray crystallog-
raphy. Organosilatranes were initially screened for their pharmacokinetic profile
using absorption, distribution, metabolism, excretion and toxicity (ADMET) tools
and then explored for their antimicrobial activities, with compound 9 emerging as
the most potent antimicrobial agent. Compounds 1–3 and 7–9 also underwent thor-
ough computational analysis by applying the density functional theory (DFT)
approach with B3LYP/6‐31G(d) level of theory and the results were found to be con-
sistent with the experimental data. Several DFT‐based descriptors were also evalu-
ated providing a valuable insight into molecular stability and reactivity.
Email: gjpsingh@pu.ac.in
Mario Wreidt, Department of Chemistry and
Biomolecular Science, Box 5810, Clarkson
University, Potsdam, New York 13699, U.S.A.
Email: mwriedt@clarkson.edu
KEYWORDS
antimicrobial activity, click approach, organosilatrane, photophysical study, quantum
chemical calculation
1
|
INTRODUCTION
have been extensively investigated due to their excellent bio-
logical properties credited to the presence of azomethine
[
4–9]
Infectious diseases are still a major concern for public health,
despite incredible progress in the field of medical sciences.
functionality.
Triazolyl Schiff base derivatives are
[
1]
hybrids with a heterocyclic core and an azomethine linkage
[
10]
Antimicrobial resistance, particularly methicillin‐resistant
Staphylococcus aureus and vancomycin‐resistant Entero-
cocci, has resulted in a more sensitive outbreak of this catas-
trophe in recent decades. This emergence motivates the
discovery of new classes of antimicrobial agents with multi-
ple actions, high bioavailability and minimum resistance to
curb the high rates of morbidity and mortality. It is beneficial
to instigate this development through fragments with poten-
providing an excellent pharmacological role.
Much work
has been published describing 1,2,4‐triazole Schiff base
[
11]
derivatives,
rather less has been done regarding 1,2,3‐tri-
[2]
azole Schiff base compounds.
Interest in 1,2,3‐triazole compounds has flourished
within the realm of heterocyclic compounds in the last few
decades because of their ready accessibility, incredible stabil-
ity and broad spectrum of pharmacological activities such as
antibacterial, anticancer, antifungal, anti‐HIV and anti‐
[
3]
tial drug profiles. In this context, Schiff base derivatives
Appl Organometal Chem. 2017;e3728.
wileyonlinelibrary.com/journal/aoc
Copyright © 2017 John Wiley & Sons, Ltd.
1 of 9
https://doi.org/10.1002/aoc.3728

2
of 9
SINGH ET AL.
[12–18]
tubercular properties.
Also, this nitrogen‐bearing ring
sulfate (Finar), 3‐chloropropyltriethoxysilane (Aldrich) and
has also found tremendous applications as bioisostere of
amide, peptide, double bond and aromatic rings.
Bromotris(triphenylphosphine)copper(I)
(Aldrich) were used as received. Schiff bases and 3‐AzPTES
(CuBr(PPh ) )
3 3
[
19–22]
Another impressive fragment considered to replenish the
arsenal of antimicrobial agents is the silatrane template which
is an intramolecularly coordinated silicon complex with
penta‐coordinated trigonal bipyramidal geometry at the sili-
con atom, a unique tricyclic atrane ring and a trans‐annular
dative bond between silicon and nitrogen that leads to
hypercoordination in the silatrane resulting in its exceptional
were synthesized using known procedures from the litera-
[
32,33]
ture.
Infrared (IR) spectra were obtained neat with a
Thermo Scientific Fischer spectrometer. CHN analyses were
conducted with a PerkinElmer model 2400 CHNS elemental
analyzer and a Thermo Scientific Flash 2000 organicelemental
analyzer. Mass spectral measurements (electrospray ionization
sourcewithcapillaryvoltageof2500V)werecarriedoutwith a
[23,24]
1
chemical and physical properties.
Its very broad appli-
VG Analytical (70‐S) spectrometer. Multinuclear NMR ( H,
[
25]
13
cation in medicine, agriculture and veterinary sciences
C) spectra were recorded with a Bruker Advance II 400 and
has contrived it to show even more exciting future endeavors.
The ‘molecular hybridization’ approach is followed for
the design of Schiff base‐type triazole‐encapped
organosilicon compounds. This strategy aims at the integra-
tion of distinct chemical entities into a hybrid template which
may show properties unattainable by separate precursors thus
a Jeol (AL 300 MHz) spectrometer usingCDCl as internal ref-
3
erence and chemical shifts were recorded relative to
tetramethylsilane. J values are given in Hz. The following
abbreviationsareused:s,singlet;d,doublet;q,quartet;t,triplet;
m, multiplet. Melting points were uncorrected and measured
with a Mel Temp II device using sealed capillaries.
[26]
meeting the needs of versatile chemistry.
Among various
protocols available, the widely growing ‘click silylation’
methodology based on Huisgen's 3 + 2 cycloaddition that is
already established owing to its incredible efficiency, excel-
2
.2 | General procedure for synthesis of diacetylenic
[
27]
schiff bases (1–3)
lent regioselectivity and admirable biocompatibility
is
pursued for the development of new and efficient chemother-
apeutic agents.
Schiff base (1.0 equiv.) was initially dissolved in 5 ml of
dimethylformamide (DMF) followed by the addition of anhy-
drous K CO (3.0 equiv.). The resulting suspension was
[
28]
In the work reported here, salicylaldehyde was used as a
precursor to synthesize acetylenic Schiff bases (1–3). These
terminal alkynes on ‘click silylation; with 3‐
azidopropyltriethoxysilane (3‐AzPTES) resulted in triazole‐
encapped silanes (4–6) which were transesterified with
triethanolamine to derive the ultimate silatranes (7–9). The
intermediate Schiff base‐linked acetylenes and organosilanes
can be meticulously exploited in the field of medicinal and
2
3
stirred for 30 min at room temperature and was then cooled
to 0 °C. To this, propargyl bromide (2.6 equiv.) was subse-
quently added dropwise over a period of 10 min under stir-
ring and the resulting mixture was allowed to stir at room
temperature for 16 h. The reaction was monitored by TLC,
and on completion, quenched by ice‐cold water. Precipitation
occurred on addition of ice‐cold water and the precipitates so
obtained were filtered, washed with water and recrystallized
from MeOH to afford the crystalline brown Schiff base bis‐
acetylenes (SBBA) in high yields. The supporting informa-
tion gives the detailed spectroscopic data of SBBA.
[29,30]
material chemistry, respectively.
In continuation of our
[31]
studyofatranechemistry, weobtainedneworganosilatranes
whichwereinitiallyscreenedfor their pharmacokinetic proper-
ties following the absorption, distribution, metabolism, excre-
tion and toxicity (ADMET) approach and then investigated
for their antimicrobial activities and photophysical properties.
Further, to gain an insight into the electronic structure of the
compounds, quantum chemical calculations employing the
density functional theory (DFT) approach were carried out
using the Gaussian03 program.
2
.3 | General procedure for synthesis of schiff base‐
linked bis‐organotriethoxysilanes (4–6)
Schiff base‐linked diyne (1.0 equiv.) was added to a 1:1 tetra-
hydrofuran (THF)–Et N solvent mixture in a two‐necked
3
round‐bottomed flask, and the mixture was stirred for
1
5 min at room temperature. Slow addition of 3‐AzPTES
2
2
|
EXPERIMENTAL
(
(
2.0 equiv.) was done followed by CuBr(PPh3)3 catalyst
0.01 mmol). The mixture was stirred at 60 °C for 5 h. The
.1 | Materials and methods
reaction was then brought to room temperature. The solvents
were evaporated under reduced pressure followed by the
addition of hexane. The reaction mixture was then filtered,
and concentration of filtrate under reduced pressure afforded
the viscous brown Schiff base bis‐silane (SBBSi) in good
yield. The detailed characterization of SBBSi is given in the
supporting information.
All the syntheses were carried out under dry nitrogen atmo-
sphere using a vacuum glass line. The organic solvents were
dried according to standard procedures. Salicylaldehyde
(
(
CDH) was vacuum distilled prior to use. Propargyl bromide
80%intoluene;Aldrich),hydrazinehydrate,ethylenediamine,
o‐aminophenol, potassium carbonate (Thomas), sodium

SINGH ET AL.
3 of 9
2
.4 | General procedure for synthesis of Schiff base‐
J = 8.3 Hz, 2H, H3, H3’), 7.58 (m, 2H, Tz─H), 7.65 (m,
4H, H4, H4’, H6, H6’), 8.08 (s, 2H, ─CH═N). C NMR
1
3
linked bis‐organosilatranes (7–9)
(
75 MHz, CDCl , 25 °C, δ, ppm): 13.1 (SiCH ), 26.4
3
2
To a stirred solution of silane (1.0 equiv.) in toluene (30 ml)
in a two‐necked round‐bottomed flask fitted with a Dean–
Stark assembly was added triethanolamine (2.0 equiv.)
dropwise followed by the addition of a catalytic amount of
KOH. The mixture was refluxed for 4 h in order to
azeotropically remove ethanol formed during the reaction.
Then the solvent was removed under reduced pressure
followed by the addition of 15 ml of hexane. The contents
were left stirring overnight after which the product was iso-
lated as a dark brown solid which was filtered under nitrogen
and dried under vacuum to afford Schiff base bis‐silatranes
(
CCH C), 40.3 (NCH CH N), 51.5 (OCH CH N), 53.5
2 2 2 2 2
(N CH ), 57.9 (OCH CH ), 63.2 (OCH ), 113.5 (C3, C3’),
3
2
2
2
2
1
1
(
8
21.5, 136.2 (Tz─C), 123.0 (C5, C5’), 126.1 (C1, C1’),
28.7 (C6, C6’), 129.0 (C4, C4’), 158.9 (CH═N), 161.0
C2, C2’). MS: m/z (relative abundance (%), assignment):
+
61 (100, [M + H] ).
2
.4.3 | Synthesis of (E)‐2‐((1‐(3‐(silatranyl)propyl)‐1H‐1,2,3‐
triazol‐4‐yl)methoxy)‐N‐(2‐((1‐(3‐(silatranyl)propyl)‐1H‐1,2,3‐
triazol‐4‐yl)methoxy)benzylidene)aniline (9)
The quantities used were: triethanolamine (0.38 g,
2
1
(SBBSa).
.55 mmol), 6 (1.0 g, 1.28 mmol). Yield 0.97 g (91%); m.p.
40–142 °C. Anal. Calcd for C H N O Si (%): C, 55.13;
37
51
9
8
2
2
.4.1 | Synthesis of (1E,2E)‐1,2‐bis(2‐((1‐(3‐(silatranyl)pro-
H, 6.38; N, 15.64. Found (%): C, 55.09; H, 6.29; N, 15.59.
IR (neat, cm ): 580 (N → Si), 753, 1094 (Si─O), 938
pyl)‐1H‐1,2,3‐triazol‐4‐yl)methoxy)benzylidene)hydrazine (7)
−
1
The quantities used were: triethanolamine (0.37 g,
(
(
2
C─C), 1120, 1239 (O─CH ), 1362 (CH ─N), 1618
2 2
2
.46 mmol), 4 (1.0 g, 1.23 mmol). Yield 0.94 g (89%); m.p.
charring above 200 °C. Anal. Calcd for C H N O Si
2
1
C═N), 2933 (C═C─H). H NMR (400 MHz, CDCl3,
5 °C, δ, ppm): 0.38 (m, 4H, ─SiCH ─), 1.95 (m, 4H,
3
8
52 10
8
2
(
6
%): C, 54.79; H, 6.29; N, 16.81. Found (%): C, 54.68; H,
.17; N, 16.78. IR (neat, cm ): 571 (N → Si), 753, 1043
─
CCH C─), 2.77 (t, J = 5.8 Hz, 12H, ─CH N─), 3.71 (t,
2
2
−
1
J = 5.8 Hz, 12H, ─OCH CH ─), 4.25 (t, J = 7.5 Hz, 2H,
─
4
4
(
1
2
2
(
1
2
Si─O), 909 (C─C), 1082, 1236 (O─CH ), 1349 (CH ─N),
2 2
N CH ─), 4.31 (t, J = 7.5 Hz, 2H, ─N CH ─), 5.29 (s,
3 2 3 2
1
614 (C═N), 2874 (C═C─H). H NMR (300 MHz, CDCl ,
3
H, ─OCH ─), 6.95–7.01 (m, 2H, H9, H11), 7.04–7.13 (m,
2
5 °C, δ, ppm): 0.30 (m, 4H, ─SiCH ─), 1.91 (m, 4H,
2
H, H3, H5, H10, H12), 7.42 (t, J = 4.2 Hz, 1H, H4), 7.64
─
CCH C─), 2.66 (t, J = 5.8 Hz, 12H, ─CH N─), 3.63 (t,
2 2
s, 1H, Tz─H), 7.65 (s, 1H, Tz─H), 8.19 (d, J = 7.7 Hz,
J = 5.8 Hz, 12H, ─OCH CH ─), 4.27 (t, J = 7.3 Hz, 4H,
13
2
2
H, H6), 8.88 (s, 1H, ─CH═N). C NMR (101 MHz,
─
N CH ─), 5.23 (s, 4H, ─OCH ─), 6.92 (t, J = 7.6 Hz,
3 2 2
CDCl , 25 °C, δ, ppm): 13.2 (SiCH ), 26.3 (CCH C), 50.9
3
2
2
2H, H5, H5’), 7.04 (d, J = 8.2 Hz, 2H, H3, H3’), 7.20–
(
(
(
1
1
OCH CH N), 53.4 (N CH ), 57.5 (OCH CH ), 62.7
2 2 3 2 2 2
7
.22 (m, 2H, H4, H4’), 7.64 (s, 2H, Tz─H), 8.03 (d,
OCH ), 63.8 (OCH ), 112.6 (C3), 114.8 (C12), 120.8
2
2
13
J = 7.7 Hz, 2H, H6, H6’), 8.95 (s, 2H, ─CH═N).
C
C9), 121.3 (C5), 122.0 (C11), 122.8 (C10), 125.2, 126.3,
43.0, 143.3 (Tz─C), 127.9 (C1), 128.4 (C6), 132.0 (C4),
32.7 (C7), 151.1 (C8), 157.2 (CH═N), 158.3 (C2). MS:
NMR (75 MHz, CDCl , 25 °C, δ, ppm): 13.0 (SiCH ), 26.4
3
2
(CCH C), 51.3 (OCH CH N), 53.4 (N CH ), 57.8
2 2 2 3 2
(
OCH CH ), 63.1 (OCH ), 113.0 (C3, C3’), 121.5 (C5,
2
2
2
m/z (relative abundance (%), assignment): 806 (100,
[
C5’), 123.1 (C1,C1’), 123.6, 132.7 (Tz─C), 127.9 (C6,
C6’), 128.7 (C4, C4’), 157.5 (CH═N), 158.2 (C2, C2’).
+
M + H] ).
MS: m/z (relative abundance (%), assignment): 833 (100,
+
2
.5 | X‐ray crystallography
[M + H] ).
Data collections were performed on single crystals coated
with Paratone‐N oil and mounted on Kapton loops. Single‐
crystal X‐ray data of all compounds were collected with a
Bruker Kappa Apex II X‐ray diffractometer equipped with a
Mo X‐ray source (sealed tube, λ = 0.71073 Å) and an APEX
II CCD detector equipped with an Oxford Cryosystems Desk-
top Cooler low‐temperature device. The APEX‐II software
1
2
1
2
2
.4.2 | Synthesis of (N E,N E)‐N ,N ‐bis(2‐((1‐(3‐(silatranyl)
propyl)‐1H‐1,2,3‐triazol‐4‐yl)methoxy)benzylidene)ethane‐1,2‐
diamine (8)
The quantities used were: triethanolamine (0.36 g,
.38 mmol), 5 (1.0 g, 1.19 mmol). Yield 0.97 g (92%); m.p.
83–185 °C. Anal. Calcd for C H N O Si (%): C,
5.79; H, 6.55; N, 16.27. Found (%): C, 55.71; H, 6.56; N,
6.19. IR (neat, cm ): 575 (N → Si), 749, 1087 (Si─O),
39 (C─C), 1161, 1238 (O─CH ), 1376 (CH ─N), 1617
C═N), 2929 (C═C─H). H NMR (400 MHz, DMSO,
5 °C, δ, ppm): 0.88 (m, 4H, ─SiCH ─), 1.87 (m, 4H,
CCH C─), 2.82 (t, J = 5.9 Hz, 12H, ─CH N─), 3.66 (t,
2 2
2
1
5
1
9
(
2
─
J
─
4
0
56 10
8
2
suite was used for data collection, cell refinement and reduc-
−1
[34]
tion.
Absorption corrections were applied using
[
35]
SADABS.
Space group assignments were determined by
2
2
1
examination of systematic absences, E‐statistics and succes-
sive refinement of the structures. Structure solutions were
performed using intrinsic phasing methods implemented with
2
[
36]
=
5.9 Hz, 12H, ─OCH CH ─), 3.90 (m, 4H,
ShelXT
and structure refinements were performed by
2
2
2
NCH CH N), 4.26 (t, J = 7.5 Hz, 4H, ─N CH ─), 5.21
least‐squares refinements against |F| followed by difference
Fourier synthesis using ShelXL, both softwares being part
2 2 3 2
[
37]
(
s, 4H, ─OCH ─), 6.98 (m, 2H, H5, H5’), 7.25 (d,
2

4
of 9
SINGH ET AL.
[
38]
1
13
of the ShelX program package.
All non‐hydrogen atoms
spectroscopic techniques (IR, NMR ( H, C) and mass)
and elemental analysis. Additionally, molecular structures
of 1, 2, 3 and 7 were authenticated using X‐ray crystallogra-
phy. The spectroscopic data and the X‐ray results are
discussed in the supporting information.
were refined with anisotropic displacement parameters. The
C─H atoms were positioned with idealized geometry and
were refined with fixed isotropic displacement parameters
(
U (H) = −1.2U (C)) using a riding model with
eq
eq
dC─H = 0.95 Å (aromatic) and 0.99 Å (methylene). For 7, car-
bon atoms C34, C36 and C38 of ─CH CH O─ unit were dis-
2
2
3
.2 | Photophysical studies
ordered over two positions (C34 and C34’; C36 and C36’;
C38 and C38’) with site occupancy factors of 0.7 and 0.3.
CCDC‐1487223 (1), −1483051 (2), −1482985 (3) and
Photophysical studies were carried out with 10− M concen-
tration of compounds in methanol as solvent. Figure 1 shows
the UV–visible spectra for compounds 7–9. The compounds
display marked difference in their absorption wavelengths.
The absorption spectra of 7 and 8 exhibit two absorption
peaks corresponding to π → π* electronic transition. The
major bands in the spectra of 7 and 8 appear at 341 and
4
−
1482986 (7) contain the supplementary crystallographic
data for this paper. These data can be obtained free of charge
from the Cambridge Crystallographic Data Centre via www.
ccdc.cam.ac.uk.
3
72 nm while minor bands are located at 292 and 303 nm,
respectively, as detailed in Table S1. The minor bands repre-
sent weak electronic transitions which may be due to the
presence of minor tautomers. Although the hydroxyl groups
have been protected in this case, the tautomers may exist in
the presence of methanol acting as hydrogen bond donating
3
3
|
RESULTS AND DISCUSSION
.1 | Synthesis
Schiff bases were used as starting materials for the synthesis
of SBBSi (4–6) and SBBSa (7–9) as shown in Scheme 1.
Firstly, Schiff bases were transformed into their acetylenic
derivatives SBBA (1–3) by the reaction with propargyl bro-
mide assisted by base K CO in DMF as solvent. These
Schiff base‐modified terminal alkynes were then coupled
with 3‐AzPTES via copper‐catalyzed azide–alkyne cycload-
dition reaction to form 1,2,3‐triazole blended triethoxysilanes
SBBSi (4–6). This methodology is based on the highly
efficient CuBr(PPh ) –THF–Et N system. Finally, transes-
solvent. However, silatrane
8
displays
a
marked
bathochromic as well as hyperchromic shift in its spectrum
as compared to silatrane 7. This shift may be attributed to
the more planar conformation of this compound resulting in
a large red shift of the long‐wavelength absorption maximum.
SBBSa 9 absorbs with a single absorption peak at 326 nm.
The hypsochromic accompanied by a hypochromic shift for
this compound may be associated with the reduced symmetry
of this silatrane.
2
3
3
3
3
terification of the synthesized triethoxysilanes with
triethanolamine in the presence of a catalytic amount of
KOH in toluene yielded SBBSa (7–9) in good yields. These
silatranes were observed to be hydrolytically more stable than
their corresponding triethoxysilane analogues. All the syn-
thesized compounds were well characterized using various
3
.3 | X‐ray crystallography
Single crystals of compounds 1, 2, 3 and 7 were grown by
slow evaporation of corresponding solutions in chloroform
at room temperature. All atoms are located in crystallograph-
ically independent general positions. All complexes are of
discrete monomer type. The detailed crystallographic data
and structure refinement parameters for 1, 2, 3 and 7 are sum-
marized in Table S2. An ORTEP view of compounds 1, 2, 3
and 7 with atom labeling scheme is given in Figures S1–S4
(supporting information).
Single‐crystal X‐ray data reveal that compound 1 crystal-
lizes in monoclinic space group P2 /c with two formula units
1
and unit cell dimensions of a = 4.1277(5) Å, b = 9.5827(1)
3
Å, c = 20.318(2) Å, V = 803.18(16) Å , ρ = 1.308 g cm
.
calc
−3
A total of 9743 reflections were calculated of which
2
007 were independent and 1201 (F > 4σ(F )) were consid-
0
0
ered and used in the structure analysis and refinement. Com-
pound 2 crystallizes in the orthorhombic space group Pbca
with four formula units and unit cell dimensions of
a = 12.239(4) Å, b = 8.737(4) Å, c = 17.081(7) Å, Z = 4,
SCHEME 1 Reagents and conditions: (i) ethanol, 1–1.5 h, reflux; (ii)
3
−3
V = 1826.5(1) Å , ρ
= 1.252 g cm . A total of 14 326
calc
propargyl bromide, K
CuBr(PPh , THF/Et
reflux, 5 h
2
CO
3
, DMF, 25 °C, 16 h; (iii) 3‐AzPTES,
reflections were calculated, 2271 of which were independent
3
)
3
3
N, 60 °C, 5 h; (iv) triethanolamine, KOH, toluene,
and 1822 (F > 4σ(F )) were considered and used in the
0
0

SINGH ET AL.
5 of 9
site and oxygens of tripodal trianionic unit occupying equato-
rial positions (Figure 3A). The transannular N → Si bond is
significantly shorter than the sum of van der Waals radii,
thereby suggesting coordinate bonding between the two.
The Si─N bonds and angles around Si are in accord with lit-
[
39]
erature values. In terms of the percentage, trigonal bipyra-
midal character is also calculated by taking into account the
[
40]
Tamao parameters.
The perspective crystal packing view
for 7 is shown in Figure 3(B).
3
.4 | Quantum chemical studies
3
.4.1 | HOMO–LUMO energy gaps and related molecular
properties
FIGURE 1 Absorption spectra of organosilatranes 7–9
The structures of Schiff base‐linked diynes 1–3 and
organosilatranes 7–9 were optimized using DFT calculations
carried out at B3LYP/6‐31G(d) level of theory. The opti-
mized structures of SBBA and SBBSa are presented in Fig-
ures S5 and S6. HOMO–LUMO energy gaps have been
calculated as detailed in Table S3 and pictorial representa-
tions of the electron distribution are given in Figures S7
and S8. Several other parameters presented in Table 1 have
also been determined from these calculations which give us
an idea about the molecular stability and the extent of
reactivity.
structure analysis and refinement. Compound 3 is found to
crystallize in triclinic space group P‐1 and the unit cell com-
prises a = 7.026(4) Å, b = 10.053(4) Å, c = 11.529(5) Å,
α = 82.33(1)°, β = 72.31(1)°, γ = 75.88(1)°, V = 750.8(6)
3
−3
Å , ρ = 1.280 g cm . The most prominent feature of crys-
calc
tal packing in 1, 2 and 3 is the presence of C─H⋅⋅⋅O and
C─H⋅⋅⋅N interactions (for 1, C3─H3⋅⋅⋅O1 (2.842 Å;
1
(
59.4°), C1─H1⋅⋅⋅N1 (2.504 Å; 142.9°); for 2, C6─H6⋅⋅⋅O1
2.558 Å; 151.9°), C1─H1⋅⋅⋅N1 (2.329 Å; 159.7°); for 3,
C14─H14⋅⋅⋅O1 (2.975 Å; 157.3°), C1─H1⋅⋅⋅N1 (2.578 Å;
48.1°)) involving the terminal acetylene group. The C─H
HOMO and LUMO shed light on the spatial distribution
of molecular orbitals and are admirable descriptors of elec-
1
[
41]
(
(
aromatic) and acetylene groups act as donors while O
phenoxy) and N (benzamine) atoms act as acceptors, which
tron transport in molecular systems.
This information
serve to link discrete units in the supramolecular architecture
as shown in Figure 2(D)–(F).
The Schiff base‐linked triazole‐bound organosilatrane 7
crystallizes in monoclinic space group P2 /n with four for-
1
mula units and unit cell dimensions of a = 12.516(1) Å,
b = 19.377(2) Å, c = 16.820(1) Å, β = 96.35(3)°,
3
−3
V = 4054.3(5) Å , ρ
= 1.370 g cm . A total of 57 516
calc
reflections were calculated of which 10 093 were indepen-
dent and 5089 were considered, observed and employed in
structure refinements. The central Si atom achieves a coordi-
nation number of five with nitrogen atom present at the apical
FIGURE 2 Asymmetric units showing coordination environment for 1 (a),
2
(
(b) and 3 (c). Crystal packing with view along crystallographic a‐axis for 1
d) and along b‐axis for 2 (e) and 3 (f). The hydrogen atoms in (d), (e) and (f)
have been removed for clarity
FIGURE 3 (a) Asymmetric unit showing coordination environment for 7.
(b) Packing arrangement with view along crystallographic a‐axis. Note that
disorder and hydrogen atoms have been removed for clarity

6
of 9
SINGH ET AL.
TABLE 1 Global reactivity descriptors for Schiff base‐linked diynes 1–3 and organosilatranes 7–9 calculated at the B3LYP/6‐31G(d) level of theory
Ionization
Organosilatrane potential, IP (eV)
Electron affinity, Electronegativity,
Chemical
Chemical
Chemical
Electrophilicity,
EA (eV)
χ (eV)
potential, μ (eV) hardness, η (eV) softness, s (eV)
ω (eV)
1
2
3
7
8
9
0.153
0.223
0.152
3.530
3.913
3.907
0.097
0.038
0.069
2.160
1.958
2.175
0.125
0.130
0.110
2.845
2.936
3.041
−0.125
−0.130
−0.110
−2.845
−2.936
−3.041
0.028
0.092
0.042
0.685
0.978
0.866
0.014
0.046
0.021
0.342
0.489
0.433
0.279
0.092
0.144
5.908
4.407
5.339
[
43]
can assist theoretical as well as experimental chemists to fur-
ther explore synthesized compounds in the field of optics and
a compound.
All these properties can be calculated by
employing the following expressions:
[42]
biomolecular chemistry.
Figure S7 shows that HOMO in
IP þ EA
diyne 1 is allocated over both the phenyl rings and is also
somewhat extended to one of the acetylenic functionalities
while LUMO is more concentrated over the imine bonds
and is spread to a small extent over phenyl rings and one of
the alkyne groups. In the case of 2, HOMO follows a similar
pattern while LUMO is more delocalized over one of the phe-
nyl rings and no electron cloud is visualized over terminal
alkyne moieties. Electron distribution of HOMO in 3 is com-
parable to that in 1 and 2 with more electron density over the
imine bond. On the contrary, LUMO in 3 is predominantly
localized over the imine bond.
Figure S8 portrays the electronic distribution in Schiff
base‐linked organosilatranes. HOMO in 7 and 9 is
delocalized over both the phenyl rings of the Schiff base
and is also extended to one of the triazole rings, while in 8
most of the delocalization is over only one of the phenyl
and triazole rings. LUMO, on the other hand, follows an
identical pattern in 7 and 9 with the electron cloud distributed
to only one of the phenyl and triazole fragments, whereas in 8
the island of electron cloud is dispersed from entire phenyl to
triazole system. From Table S3, it is evident that Schiff base‐
linked diynes show comparatively higher HOMO–LUMO
energy gaps compared to their silatrane counterparts. In addi-
tion to this, HOMO–LUMO orbital energies can determine
several parameters like ionization potential, electronegativity,
electron affinity, chemical potential, hardness and softness of
IP ¼ −EHOMO
μ ¼ −χ
EA ¼ −ELUMO
χ ¼
2
IP−EA
s ¼
1
2η
μ2
ω ¼
2η
η ¼
2
3
.4.2 | Structural descriptions
The bond lengths and bond angles of compounds 1–3 and 7
were compared with experimental results and the theoretical
predictions correlate well with the experimental data. As
can be seen from Table 2, all the bond lengths and bond
angles of diynes 1, 2 and 3 from the crystallographic results
are in agreement with the results of the Gaussian output,
except one discrepancy seen in the bond angle C(3)–O(1)–
C(4) in the case of alkynes 1 and 2 and an additional angle
C(16)–O(2)–C(17) in alkyne 3 the computed value of which
underestimates the crystallographic result.
The computed bond lengths and bond angles of
organosilatrane 7 also tie in with the experimental values
derived from the crystallographic results (Table S4). The
measured N → Si bond length is 2.164 Ǻ that is much shorter
than the computed bond length of 2.932 Ǻ showing the
strength of this coordinate bond. The measured N → Si bond
[
44]
length also correlates with literature values.
The values of
TABLE 2 Theoretical and X‐ray crystallographic data for compounds 1–3
1
2
3
Measured
Computed
Measured
Computed
Measured
Computed
Bond lengths (Ǻ)
C(2)–C(3)
1.460
0.950
1.282
1.201
1.070
1.270
1.464
0.950
1.264
1.201
1.070
1.292
1.458
0.951
1.276
1.201
1.070
1.420
C(1)–H(1)
N(1)–C(10)
Bond angles (°)
N(1)–C(10)–H(10)
N(1)–C(10)–C(9)
C(3)–O(1)–C(4)
C(16)–O(2)–C(17)
O(1)–C(3)–C(2)
O(2)–C(17)–(C18)
119.40
121.10
118.20
—
118.30
119.88
109.25
—
118.90
122.15
118.78
—
119.98
119.95
108.89
—
119.00
121.95
115.47
116.69
109.18
107.57
121.25
118.77
109.13
109.25
108.94
109.47
113.20
—
109.54
—
112.56
—
109.80
—

SINGH ET AL.
7 of 9
bond angles O(1)–Si(1)–C(7) and N(6)–N(5)–C(19) from the
Gaussian output are greater than the X‐ray data by 12.01° and
alimentary canal to its site of action without binding to pass-
ing serum proteins and with no risk of breakdown into toxic
metabolites.
8.29°, respectively, showing more close packing in the abso-
lute configuration of the silatranes.
ADMET is an open source continuously updated data-
base that collects and administers the available ADMET
[
46]
3
.4.3
|
Molecular electrostatic potential (MEP)
allied data from the published literature.
The ADMET
properties of a molecule play an effective role in making a
prospective drug as effective as possible to the level of a
marketed drug. The molecules with inauspicious ADMET
properties are eliminated from further analysis. Intestinal
absorption of drug candidates can be accessed via human
colon carcinoma‐derived Caco‐2 and MDCK cell models.
Additionally, human intestinal absorption model and skin
permeability index play an important role in the prediction
of a drug's oral bioavailability and transdermal delivery.
Blood–brain barrier penetration can be informative of a drug
present in the central nervous system. The efficacy of a drug
is judged by the amount of unbound drug in the plasma that is
free to penetrate in the surrounding tissues that can be evalu-
ated from plasma protein binding values. The intelligent
application of these assays ultimately leads to the selection
of drug candidates with a high probability of clinical success.
The values calculated from ADMET predictor as detailed in
Table 3 clearly verify all the trialed compounds to be good
candidates for further analysis.
The electrostatic potential is a real physical property
reflecting the three‐dimensional nuclear and electronic
charge distribution of a system that can be obtained using
[45]
both theoretical and experimental methods.
The signifi-
cance of MEP surfaces can be concluded from their ability
to simultaneously present molecular size and shape as well
as electrostatic potential of a molecule in terms of color grad-
ing. MEP view is mapped at the B3LYP level of theory with
6‐31G(d) basis set with the optimized geometry of the mole-
cules using the Gaussian03 program. The color‐coded scale
ranges from red to blue. This scale precisely allocates the
regions with negative and positive potentials in the molecule
with red and blue as key indicators, respectively, while the
region of intermediate potential is designated by green and
yellow colors. From the MEP map of the diynes (Figure
S9), it can be clearly seen that a small part of the molecule
which is red‐colored representing imine bond is completely
negative making it a possible site for electrophilic attack
while the predominance of yellow and green color on the rest
of the MEP surface corresponds to a halfway potential
between the two extremes of red and blue. This shows very
little difference in electron density in different regions of
the molecule indicative of only slight variation in electroneg-
ativity of different parts. Three‐dimensional plots of MEP of
organosilatranes are illustrated in Figure S10, which reveals
that the regions having negative potential are localized over
the imine bond and near the triazole fragment, while positive
potential is spread over the remaining part of the molecule.
3
.6 | Antimicrobial assay
SBBSa 7–9 were screened in vitro for their antimicrobial
activities against six strains of bacteria and eight strains of
fungi. The selected strains of microorganisms are the most
frequent sources of human infections. The biocide assays
are reported in terms of inhibitory concentrations (IC50).
The results detailed in Tables 4 and 5 show that the com-
pounds are only moderately active against both types of
microorganisms. SBBSa 9 is found to be most potent against
four strains of fungi, i.E. candida albicans, C. krusei, C.
parapsolsis and C. glabrata. Against C. tropicalis and C.
neoformans, compounds 7 and 9 are equally potent but their
activity is much lower as compared to the standard drug
amphotericin B. However, against C. kyfer, silatrane 7 is
found to be as active as amphotericin B and thus can be con-
sidered as a potent antifungal agent.
3
.5 | Computational screening
Chemical breakthrough has led to the design of countless
prospective drug molecules possessing high in vitro potency
which might be negated by poorer physicochemical proper-
ties. The early profiling of compounds speeds up the selec-
tion of lead compounds without the wastage of considerable
resources. A drug's passage through the body can be mea-
sured in terms of these properties. Molecular bouncers pres-
ent in the liver may get induced by the drugs to lead them
to the final door of elimination through the kidneys. How-
ever, the ideal drug passes unconstrained through the
On examining the results for activity against bacterial
strains, SBBSa 9 presents better activity than the other
silatranes 7 and 8. Compounds 8 and 9 give identical results
against
Escherichia
coli,
Enterococcus
faecalis,
a
TABLE 3 Pharmacokinetic descriptors of organosilatranes 7–9
Caco‐2 cell permeability (nm s−
1
)
BBB
HIA (%)
MDCK (nm s−1
)
PPB (%)
Organosilatrane
p
Skin permeability (log K )
7
8
9
21.98
21.94
22.06
0.20
0.19
0.32
99.04
98.66
98.43
0.03
0.02
0.04
71.42
64.65
67.04
‐3.96
‐3.35
‐4.12
a
BBB: blood–brain barrier; HIA: human intestinal absorption; MDCK: Madin–Darby canine kidney; PPB: plasma protein binding.

8
of 9
SINGH ET AL.
TABLE 4 Antifungal activities of SBBSa 7–9
IC50 (μg ml−
1
)
C. albicans
(NCPF400034)
C. krusei
(NCPF44002)
C. tropicalis
(NPCPF420007)
C. parapsolsis
(NCPF450002)
C. kyfer
(NPCPF410004)
C. neoformans
(NCPF250316)
C. glabrata
(MTCC3019)
Compound
7
208
>208
215
104
>215
100.6
0.72
208
104
104
>215
100.6
1.80
>208
215
8
107.5
50.3
0.72
107.5
25.15
0.72
215
9
100.6
0.72
201.25
115.5
25.15
0.72
Amphotericin B
TABLE 5 Antibacterial activities of SBBSa 7–9
IC50 (μg ml−
1
)
E. coli
(MTCC2961)
E. faecalis
(MTCC439)
S. aureus
(MTCC3160)
V. cholerae
(MTCC3906)
S. pyogenes
(MTCC442)
L. monocytogenes
(MTCC839)
Compound
7
208
104
208
104
104
104
8
107.5
100.6
3.2
53.75
50.3
25.7
107.5
100.6
51.4
107.5
100.6
51.4
107.5
25.15
51.4
107.5
100.6
102.9
9
Rifampicin
Staphylococcus aureus, Vibrio cholerae and Listeria
monocytogenes strains of bacteria with moderate IC50 values.
However, silatrane 9 displays excellent efficacy against Strep-
tococcus pyogenes with IC50 value even less than that of the
standard drug rifampicin, thus emerging as an impressive
candidate for further analysis.
analyzed computationally by applying the DFT approach
and theoretical results were in agreement with the experimen-
tal data. In addition, several DFT‐based global reactivity
parameters were evaluated giving a detailed view of molecu-
lar stability. Further, MEP surface analysis outlines the possi-
ble regions of nucleophilic and electrophilic attack.
ACKNOWLEDGMENTS
3
.7 | Structure–activity relationship
The authors thank CSIR (New Delhi), DST‐PURSE, DST‐
SERB and UGC for providing financial support. Special
thanks are extended to Mr. Avtar Singh, SAIF, Panjab Uni-
versity, Chandigarh for NMR studies.
Organosilatrane 7 is found to be the most effective silatrane
against C. kyfer strain of fungus while silatrane 9 which is
an asymmetric bis‐silatrane is the most potent for all other
strains of fungi with the best activity against C. parapsolsis
and C. glabrata. Organosilatranes are more influential
against the bacterial strains than the fungal ones and again
silatrane 9 displays admirable results against all strains of
bacteria with the best results against S. pyogenes. On examin-
ing the activities of silatranes 7 and 8, it is observed that the
introduction of carbon chain between the two azomethine
linkages in silatrane 8 results in a decrease of activity which
is greater against the bacterial strains than the fungal strains.
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