Elena O Levina1, Nikita V Penkov2, Natalia N Rodionova3, Sergey A Tarasov3, Daria V Barykina3, Mikhail V Vener4. 1. Department of Molecular and Chemical Physics, Moscow Institute of Physics and Technology, 7 Institutskiy per., 141700 Dolgoprudny, Russia. 2. Department of Methods of Optical and Spectral Analysis, Institute of Cell Biophysics, Russian Academy of Sciences, 3 Institutskaya Street, 142292 Pushchino, Russia. 3. OOO "NPF" Materia Medica Holding, 47-1 Trifonovskaya Street, 129272 Moscow, Russia. 4. Department of Quantum Chemistry, Mendeleev University of Chemical Technology, 9 Miusskaya Square, 125047 Moscow, Russia.
Abstract
Diclofenac (active ingredient of Voltaren) has a significant, multifaceted role in medicine, pharmacy, and biochemistry. Its physical properties and impact on biomolecular structures still attract essential scientific interest. However, its interaction with water has not been described yet at the molecular level. In the present study, we shed light on the interaction between the steric hindrance (the intramolecular N-H···O bond, etc.) carboxylate group (-CO2-) with water. Aqueous solution of sodium declofenac is investigated using attenuated total reflection-infrared (ATR-IR) and computational approaches, i.e., classical molecular dynamics (MD) simulations and density functional theory (DFT). Our coupled classical MD simulations, DFT calculations, and ATR-IR spectroscopy results indicated that the -CO2- group of the diclofenac anion undergoes strong specific interactions with the water molecules. The combined experimental and theoretical techniques provide significant insights into the spectroscopic manifestation of these interactions and the structure of the hydration shell of the -CO2- group. Moreover, the developed methodology for the theoretical analysis of the ATR-IR spectrum could serve as a template for the future IR/Raman studies of the strong interaction between the steric hindrance -CO2- group of bioactive molecules with the water molecules in dilute aqueous solutions.
Diclofenac (active ingredient of Voltaren) has a significant, multifaceted role in medicine, pharmacy, and biochemistry. Its physical properties and impact on biomolecular structures still attract essential scientific interest. However, its interaction with water has not been described yet at the molecular level. In the present study, we shed light on the interaction between the steric hindrance (the intramolecular N-H···O bond, etc.) carboxylate group (-CO2-) with water. Aqueous solution of sodium declofenac is investigated using attenuated total reflection-infrared (ATR-IR) and computational approaches, i.e., classical molecular dynamics (MD) simulations and density functional theory (DFT). Our coupled classical MD simulations, DFT calculations, and ATR-IR spectroscopy results indicated that the -CO2- group of the diclofenac anion undergoes strong specific interactions with the water molecules. The combined experimental and theoretical techniques provide significant insights into the spectroscopic manifestation of these interactions and the structure of the hydration shell of the -CO2- group. Moreover, the developed methodology for the theoretical analysis of the ATR-IR spectrum could serve as a template for the future IR/Raman studies of the strong interaction between the steric hindrance -CO2- group of bioactive molecules with the water molecules in dilute aqueous solutions.
Molecular
solute–solvent interaction studies are of paramount
importance in gaining a deeper understanding of the biomolecular function
and the fundamental mechanisms involved in the conformational adaptation
in solutions.[1] Physicochemical properties
of this interaction are widely studied in various environments (i.e.,
solvents), especially in water—usually referred to as the solvent
of life.[2]NMR spectroscopy is an
important technique for investigating biomolecular
interactions and protein dynamics.[3] It
is commonly used in combined experimental and theoretical studies
to examine the interactions between polar solvents and biomolecular
functional groups,[4] the influence of solvent
dynamics on the structure of hydrogen-bonded complexes,[5,6] and the dynamics of side-chain amino groups in an aqueous solution.[7] The applicability of NMR in the investigation
of the first hydration shell of the −CO2– groups in aqueous solutions is not straightforward.[8]IR spectroscopy is another basic tool used for elucidating
the
biomolecular interactions and solvent–solute interaction studies.[9,10] Special focus is generally given to the so-called amide I, II, III,
and A regions,[11] but sometimes other regions
are also investigated.[12] Due to the strong
absorbance of water in the mid-infrared spectral region, the IR difference
spectra are used. The attenuated total reflection-infrared (ATR-IR)
mode after subtraction of the water spectrum gives the IR spectrum
of the solute,[13] if it does not form relatively
strong hydrogen bonds (H-bonds)[14] with
water molecules. As for specific strong interactions, the water spectrum
should be subtracted except a few water molecules that form relatively
strong H-bonds with a solute molecule. Their number can be estimated
if the solute is highly soluble in water. Spectral analysis of a series
of highly concentrated solutions of known density and solute’s
mass fraction allows obtaining a stoichiometricratio of solutions
under study[15,16] and, consequently, estimating
the number of water molecules in the first hydration shell.Some peculiarities of active pharmaceutical ingredients can strongly
affect the above research methodology. The first one is low solubility.
For instance, the maximum plasma concentration of anti-inflammatory
drugs[17−19] is usually lower compared to their solubility. This
stipulates the possibility of using substances with rather low solubility[20,21] for medical purposes. The second is a relatively strong interaction
between some bioactive molecules and water molecules.[22−24] Due to rather low solubility of sodium diclofenac (∼3.5 ×
10–3 mol L–1 at pH = 7.0)[25] and its relatively strong specific interaction
with water molecules, the interpretation of the ATR-IR spectrum of
its aqueous solution is not straightforward. Thus, an adequate description
of the structure of the first hydration shell and spectral features
of the aqueous solution of sodium diclofenac (NaDN) could be achieved
by combining ATR-IR and theoretical studies.Density functional
theory (DFT) based MD simulations[26,27] give a reliable
description of the local structural motifs,[28] solvation shell, and IR spectra[29−31] of the bioactive molecules
in water and polar solvents. It should
be noted that these simulations are at present computationally demanding
for systems of modest sizes (a solute and ∼50 water molecules),
and currently intractable for larger sizes (a solute and ∼1000
water molecules).[32,33] Due to low solubility of NaDN,
the ratio of 1 solute molecule to 1000 water molecules corresponds
to the highest possible concentration of the aqueous solution of NaDN[25] that makes ab initio MD simulations hardly applicable.Classical molecular dynamics (MD), Monte Carlo simulations,[34−40] and the RISM integral equation method[41,42] led to valuable
insights into the hydration structure of bioactive molecules in water.
In general, these approaches allow to compute the IR spectra.[43,44] If nonpolarizable classical force fields are used in the simulations
to obtain the IR spectra, the results should be treated with some
caution, e.g., refer to ref (45).The solvation phenomenon can be described using
implicit solvent
models.[46] In particular, the discrete-continuum
model[47] is often used for the evaluation
of the vibrational frequencies of molecules in water.[48] A serious drawback of the model is the uncertainty in the
minimum number of water molecules required to simulate the first hydration
shell in diluted aqueous solutions.[49] This
number can be estimated from the classical MD simulations. Another
significant limitation of the discrete-continuum model consists in
the absence of specific interactions between the molecules forming
the first hydration shell and the adjacent water molecules. To the
best of our knowledge, no approach that might overcome this limitation
has been proposed so far. The microsolvation model provides a semiquantitative
description of the spectral properties and the hydration shell’s
structure of bioactive molecules.[50−52] We conclude that classical
MD simulations and DFT computations of complexes of a bioactive molecule
with several water molecules may be considered as complimentary.Sodium diclofenac is a pharmaceutically active substance with pronounced
anti-inflammatory, analgesic, antipyretic, and anticancer activities.[53] Its molecular effects are associated with the
formation of hydrogen bonds between the carboxyl group of diclofenac
and side chains of Tyr-385 and Ser-530 present in COX.[54,55] However, now sodium diclofenac has limited use because of various
side effects (including gastrointestinal and cardiovascular ones)[56] arising from its nonselective action on both
cyclooxygenase isozymes (COX-1 and COX-2). Diclofenac has currently
been under intensive development by the pharmaceutical industry with
respect to its efficacy and safety, aimed at creating improved forms
of diclofenac-based drugs. For example, a released active form of
diclofenac is being studied as a possible option. It is produced by
means of a special process, which results in the high efficacy of
diclofenac in the released active form, with almost no side effects.[57] Because the pharmaceutical effects of diclofenac
primarily occur due to the hydrogen-bond interaction between its carboxyl
group and the targets (Tyr-385 and Ser-530 of the COX enzymes), it
is important to look into the involvement of this carboxyl group in
other processes, such as the formation of the hydration shell of diclofenac.
Therefore, understanding the physicochemical properties and features
of the hydration shell formation is essential for developing a form
of diclofenac that could sterically facilitate a higher pharmaceutical
efficacy (and safety). The NMR studies of NaDN solutions were used
to detect related complexes with cyclodextrin[58,59] and with calix[4]arene.[4]arene derivative and its selective interaction
with drugs (clofibric acid, diclofenac and aspirin). Eur. J. Pharm. Sci.. 2017 ">60] NMR and IR
spectroscopy techniques were used to evaluate the quality of genericNaDN tablets.[61] The IR spectrum of the
aqueous solution of NaDN has not been published yet, based on the
available data.The intramolecular N–H···O
bond and chlorine
atoms present in the adjacent benzene ring (Figure and ref (62)) cause the carboxylate group (−CO2–) observed in the diclofenac anion (DN–) to exhibit steric hindrance effect, which is characteristic
of anti-inflammatory agents.[63] This distinguishes
the DN– anion from the anions of carboxylic acids,
the hydration of which has been studied in detail.[64−66] On the other
hand, the hydration shell of the DN– anion is expected
to differ markedly from that in the amino acids, as the latter exist
in a zwitterion form in aqueous solutions.
Figure 1
Structure of the DN– ion with the intramolecular
N–H···O bond. The latter is denoted by the dotted
line. The red, blue, green, gray, and white circles represent oxygen,
nitrogen, chlorine, carbon, and hydrogen atoms, respectively.
Structure of the DN– ion with the intramolecular
N–H···O bond. The latter is denoted by the dotted
line. The red, blue, green, gray, and white circles represent oxygen,
nitrogen, chlorine, carbon, and hydrogen atoms, respectively.The objective of this work was
to examine the aforementioned interactions
in an aqueous solution of NaDN via ATR-IR spectroscopy combined with
classical MD simulations and DFT computations. Due to the existence
of moderate H-bonds between water and the −CO2–
group and rather a low solubility of NaDN, the interpretation of the
IR spectrum of the DN anion obtained after subtraction of the water
spectrum is not straightforward. An explicit consideration of the
first hydration shell of the anion is needed. Implementation of MD
facilitates the formation of a realistic model of the microsolvation,
subsequently used in the DFT computations. Our goal was to completely
isolate the interaction between −CO2– of
the DN– ion and water, allowing for a detailed analysis
of the most stable complexes and, therefore, a deeper understanding
of the strong interaction between the steric hindrance −CO2– group of bioactive molecules with water molecules
in aqueous solutions.
Results
ATR-IR
Studies
The ATR-IR spectrum
of the powder of NaDN is given in Figure . It agrees well with the available literature
data.[67] The ATR-IR spectrum of the NaDN
aqueous solution (0.4%) is also given in Figure . The spectra vary very much in the frequency
region above 1700 cm–1. Obviously, this difference
is due to the solute–solvent interaction. For instance, the
broad band around ∼3200 cm–1 corresponds
to the Ow–H stretching and is shifted to the low-frequency
region, which is typical to the systems with H-bonds between solute
and solvent.[68] A specific feature of the
ATR-IR spectrum is a number of narrow Evans-type transmission windows
(the Evans holes). The holes located at around 1000 and 1250 cm–1 are associated with perturbations between superposing
energy levels.[69,70] The hole at around 1750 cm–1 has a different nature because the IR intense bands
in the 1000 frequency region are absent in the powder spectrum (Figure , and Figure 1 in
ref (67)). It is analyzed
in Section .
Figure 2
ATR-IR spectrum
of the powder of NaDN vs the ATR-IR spectrum of
its aqueous solution (0.4%) after subtraction of the water spectrum.
ATR-IR spectrum
of the powder of NaDN vs the ATR-IR spectrum of
its aqueous solution (0.4%) after subtraction of the water spectrum.The ATR-IR spectra of 0.4% NaDN
show a good signal-to-noise ratio
(Figures and S1). The concentration of this solution is about
0.01 mol L–1, approaching the ATR-IR detection limit
for aqueous solutions.[71] Indeed, the IR
spectra of solutions with concentration <0.1% differ negligibly
from the water spectrum (Figure S2). However,
a higher detection limit could be used for individual contributions
to broad bands, particularly for water-stretching vibrations, such
as those exhibited by/observed for the quasi-free OH groups.[72] The depth of the Evans hole, located at around
1750 cm–1, decreases with decreasing concentration,
but it is clearly visible at concentration 0.2% (Figure S1). This phenomenon is discussed in the section below.
Classical MD Simulations and DFT Computations
The O1–Ow radial distribution functions
(RDFs) and the cumulative distribution functions (CDFs), where O1 is the oxygen atom of the −CO2– group and Ow is the wateroxygen, obtained by MD simulations,
are given in Figure a. According to the CDF, the average number of water molecules around
the oxygen (atom/atoms) concerned is ∼3, which agrees with
the literature data.[73] To estimate the
average number of water molecules around the −CO2– group, the C–Ow RDF and CDF
are also computed (Figure b). The target value is ∼6. According to ref (64), the carboxylate ion has
about 7 strongly bound water molecules in the first hydration layer.
The reasons for this difference are the steric hindrance caused by
the formation of an intramolecular H-bond in the DN– anion (Figure ),
and variations in the mutual orientation of the benzene rings. The
latter is discussed in Section .
Figure 3
(a) O1–Ow radial distribution functions
(RDFs) and cumulative distribution functions (CDFs) obtained for aqueous
NaDN solutions (∼1.7 and ∼0.4%), where O1 is the oxygen atom of the −CO2– group and Ow is the water oxygen. (b) C–Ow RDF and CDF obtained for aqueous NaDN solutions (∼1.7
and ∼0.4%), where C is the carbon atom of the −CO2– group and Ow is the water oxygen.
(a) O1–Ow radial distribution functions
(RDFs) and cumulative distribution functions (CDFs) obtained for aqueous
NaDN solutions (∼1.7 and ∼0.4%), where O1 is the oxygen atom of the −CO2– group and Ow is the wateroxygen. (b) C–Ow RDF and CDF obtained for aqueous NaDN solutions (∼1.7
and ∼0.4%), where C is the carbon atom of the −CO2– group and Ow is the wateroxygen.In the next step, the microsolvation
process of the DN– ion is studied using DFT computations.
Metric parameters of the
intramolecular N–H···O bond in the DN–·nH2Ocomplexes, where n varies from 0 to 5, are given in Table . Due to the strength and targeted nature
of intermolecular H-bonds, only a few low-energy structures for n > 2 are available. When n = 3 and
4,
several conformers are localized; they differ by the mutual orientation
of water molecules and the number of H-bonds (Figures S3 and S4). Increasing the number of the water molecules
shifts the bridging proton from the oxygen to nitrogen atoms. This
shift leads to an extension of the N···O distance and
the distortion of the intramolecular H-bond. At n = 5, the intramolecular N–H···O bond becomes
rather long (the N···O distance is larger than 2.75
Å), and strongly nonlinear (the N–H···O
angle is ∼150°), see Table . At least one relatively short (strong) intermolecular
O···H–Ow bond, where Ow is the oxygen atom of water molecule, exists in the complexes with n > 1 (Table ).
Table 1
Metric Parameters of the Intramolecular
N···H···O Bond and the Shortest Intermolecular
O···H–Ow Bond in the DN–·nH2O Complexesa Evaluated Using DFT Computations
parameter
n = 0
n = 1
n = 2
n = 3
n = 4
n = 5
O···N, Å
2.627
2.547
2.722
2.737
2.782
2.808
O–H (H–N),b Å
1.030
1.071
1.041
1.037
1.031
1.028
O···H···N, deg
166.4
167.9
154.6
153.4
151.1
150.2
O···Ow, Å
2.916
2.713
2.704
2.658
2.686
O···H–Ow, deg
157.7
173.6
175.5
176.5
175.8
see Figure ; ‘w’
denotes the oxygen atom
of the water molecule.
at n > 1 the bridging
proton locates near the nitrogen atom.
see Figure ; ‘w’
denotes the oxygen atom
of the water molecule.
Figure 4
Global-minimum
structures of the DN–·nH2O complexes: (a) n = 1; (b) n = 2; (c) n = 3; (d) n = 4; and
(e) n = 5. Hydrogen bonds are highlighted
with light blue dotted lines. Chlorine contacts are highlighted with
red dotted lines. See the caption to Figure for color coding.
at n > 1 the bridging
proton locates near the nitrogen atom.To identify differences in the microsolvation of the
−CO2– group in DN– and acetate
(CH3CO2–) anions, the structures
of the DN–·nH2O
and CH3CO2–·nH2Ocomplexes[65,74] with n = 1, 2, 3, 4, and 5 are compared (see the Supporting Information). Briefly, the following hydration shell features
are found for the global-minimum structure of DN–·nH2Ocomplexes with n = 2, 3, 4, and 5. (1) Close spatial orientation of water molecules.
The n – 1 water molecules form at least two
intermolecular H-bonds within a complex with a certain n. (2) Formation of a R33(8)[75] motif by two water molecules and the −CO2– group linked by a three H-bond interaction. (3)
A relatively short (strong) intermolecular O···H–Ow bond: O···Ow is less than ∼2.7
(Table ).According
to the DFT computations, for n ≥
2, two or three water molecules form a H-bond with the carboxyl group
of the DN– ion (Figures and S1). This is consistent with the results of MD
simulations, which show that the average number of water molecules
directly interacting with the oxygen atom of the −CO2– group is ∼3. Furthermore, the structure
of H-bonded complexes demonstrated by the DFT computations agrees
with the results of MD simulations (cf. Figures and 5). Both cases
indicate the occurrence of the R33(8) motif.
Figure 5
Snapshots of several H-bonded complexes of the DN– ion and water molecules shown by the MD simulation of 0.4% aqueous
solution. Trajectory length = 1 ns. The H-bonds are given by the dotted
lines. The corresponding data for 1.7% solution is given in the Supporting
Information (Figure S5). See the caption
to Figure for color
coding.
Global-minimum
structures of the DN–·nH2Ocomplexes: (a) n = 1; (b) n = 2; (c) n = 3; (d) n = 4; and
(e) n = 5. Hydrogen bonds are highlighted
with light blue dotted lines. Chlorinecontacts are highlighted with
red dotted lines. See the caption to Figure for color coding.Snapshots of several H-bonded complexes of the DN– ion and water molecules shown by the MD simulation of 0.4% aqueous
solution. Trajectory length = 1 ns. The H-bonds are given by the dotted
lines. The corresponding data for 1.7% solution is given in the Supporting
Information (Figure S5). See the caption
to Figure for color
coding.Theoretical IR spectra of the
DN–·3H2O complex corresponding to
the global-minimum structure with
a zero-point energy correction are used for a tentative assignment
of the ATR-IR spectrum of the aqueous solution of sodium diclofenac
(Table S2). This approach gives reasonable
description of the most IR intensive bands in the experimental spectrum
(Figure ). To interpret
several low-intensive bands, the literature data should be used. The
low intensive band at around 2330 cm–1 is associated
with the asymmetric stretch of the CO2 molecules, which
are absorbed by the solution from the air.[76] The weak broad band near 2200 cm–1 is caused by
the asymmetric stretching vibration of the N–H···O
bond.[12,77]
Figure 6
ATR-IR spectrum of aqueous solution of NaDN
(0.4%) after subtraction
of the water spectrum vs theoretical IR spectrum of the global-minimum
structure of the DN–·3H2O complex.
ATR-IR spectrum of aqueous solution of NaDN
(0.4%) after subtraction
of the water spectrum vs theoretical IR spectrum of the global-minimum
structure of the DN–·3H2O complex.
Discussion
Now we will focus on the deep and narrow Evans hole located at
around 1750 cm–1 (Figure ). It is known that Fermi resonance is observed
if the OH stretch or bending vibrations of proton donor forming H-bond
is superposed with an overtone of proton’s donor internal vibration.[78−80] (The internal vibration is understood as the wagging vibrations
of a polyatomic molecule, which forms an H-bond complex). Usually,
Fermi resonance in the OH stretch region of liquid- or gas-phase systems
with H-bonds of different strength are investigated.[81−86] The wagging vibrations of water molecules H2Ow1 and H2Ow2, respectively, are located at around
800–900 cm–1 (Table ). Overtones of these vibrations will superpose
with the stretch vibration of water molecule forming the shortest
H-bond with the −CO2– group (Table S2). As a result, a hole is observed in
the IR spectrum of aqueous solution of sodium diclofenac at around
1750 cm–1. It is clearly visible at concentration
0.2% (Figure S1). This concentration is
below 0.01 mol L–1, and the detectability of the
hole is associated with the relatively short (strong) intermolecular
H-bond formed by the water molecule, which is part of the R33(8) motif (Figure , Table ).
Table 2
Theoretical Values of Metric Parameters
of the Intermolecular H-Bonds Forming the Eight-Member Ring in the
DN–·nH2O Complexes,a Where n = 2, 3, 4, and 5b
n = 2
n = 3
n = 4
n = 5
distance R, angle ∠
R(O···Ow1), Å (∠OHOw1, deg)
2.892 (169.8)
2.704 (175.5)
2.658 (176.5)
2.686 (175.8)
R(O···Ow2), Å (∠OHOw2, deg)
2.713 (173.6)
2.789 (174.1)
2.902 (165.2)
2.922 (164.0)
R(Ow1···Ow2), Å (∠Ow1HwOw2, deg)
2.971 (157.4)
2.890 (155.6)
2.944 (149.4)
2.946 (150.0)
vibration
σ(Hw–Ow1–Hw), cm–1c
1717 (71)
1682 (174)d
1671 (150)
1671 (92)
σ(Hw-Ow2-Hw), cm–1
1690 (278)
1737 (77)
1730 (73)d
1726 (68)
ω(Hw-Ow1-Hw), cm–1
738 (136)
902 (181)
939 (127)
901 (126)
ω(Hw-Ow2-Hw), cm–1
939 (87)
823 (177)
816 (157)d
801 (202)
See Figure .
Harmonic frequencies
and IR intensities
of the selected vibrations. σ and ω denote the bending
and wagging vibrations, respectively.
IR intensities (kM mol–1) are given
in parentheses.
Strongly
coupled to σ(Hw–Ow3–Hw).
Figure 7
Eight-member
ring in the global-minimum structure of the DN–·nH2O complexes: (a) n = 2, (b) n = 3, and (c) n = 4 and 5. H-bonds forming
the R33(8) motif
are given by dotted lines.
Eight-member
ring in the global-minimum structure of the DN–·nH2Ocomplexes: (a) n = 2, (b) n = 3, and (c) n = 4 and 5. H-bonds forming
the R33(8) motif
are given by dotted lines.See Figure .
Figure 8
Formation of the intramolecular
N–H···O bond
in the DN– ion during the MD simulations for its
0.4% (upper panel) and 1.7% (lower panel) aqueous solutions. The trajectory
lengths are 10 ns in both cases. Pairs of heavy atoms forming the
H-bond are indicated on the right.
Harmonic frequencies
and IR intensities
of the selected vibrations. σ and ω denote the bending
and wagging vibrations, respectively.IR intensities (kM mol–1) are given
in parentheses.Strongly
coupled to σ(Hw–Ow3–Hw).We conclude that
a specific feature of the hydration shell structure
is the eight-atom ring (the R33(8) motif[75,87]) formed by the two water molecules and the −CO2– group of the diclofenac anion that interact with
each other by the three H-bonds. Both water molecules form two H-bonds.
One molecule forms two H-bonds as a proton donor and a proton acceptor,
another forms two H-bonds as proton donors. The bending and wagging
vibrations of water molecules may indicate the presence of the H-bonded
water.[88] The bending vibration of the first
molecule and the wagging vibration of the second molecule shift to
blue in comparison with the corresponding vibrations of the “free”
water molecule, in accord with the literature data.[89] Overtone of the wagging vibration is superposed with the
bending vibration caused the hole in the IR spectrum. We attributed
this hole to the relatively strong specific solute–solvent
interaction. The point is that the R33(8) motif
does exist in the local-minimum structures of the DN–·3H2O and DN–·3H2O complexes (Figures S3 and S4).Crystallographic data are a valuable source of information on the
energy and geometric features of noncovalent interactions.[90−92] Screening of the Cambridge Structure Database[93] shows that the considered R33(8)
motif occurs in 31 crystals, including pharmaceutical solvates and
co-crystals, e.g., norfloxacin dihydrate,[94,95] sparfloxacin trihydrate,[96] and enrofloxacinium
dioxalate hexahydrate.[97]Another
specific feature of NaDN hydration is the steric hindrance
effect. The MD simulations show that the quasi-linear N–H···O
bond occurs frequently in the DN– ion (the N···O
distance is less than 2.75 Å, the N–H···O
angle is greater than 160°) during MD simulations at both concentrations
concerned (see Figure ). The formation of intramolecular N–H···O
bonds of ring size 7 is quite a rare event.[98,99] Usually, intramolecular N–H···O bonds of ring
size 6[100] with the strongly nonlinear N–H···O
moiety[101] are presented.Formation of the intramolecular
N–H···O bond
in the DN– ion during the MD simulations for its
0.4% (upper panel) and 1.7% (lower panel) aqueous solutions. The trajectory
lengths are 10 ns in both cases. Pairs of heavy atoms forming the
H-bond are indicated on the right.Mutual orientation of benzene rings might have a significant
role
in the COX-2 receptor inhibition.[54] According
to ref (62), the structure
of diclofenac, which is able to inhibit COX-2 (with the C–C–N–C
dihedral angle of the −60°, see Figure in ref (62)), is not stable in the gas-phase ab initio simulations.
In the case of MD simulations of water solutions, various C–C–N–C
dihedral angles were observed (see Figure S6), including oscillations around −60°. For a more accurate
description of this effect on −CO2– solvation, which is beyond the scope of this study, further research
is needed.Very recently, the IR difference spectrum for the
amide A band
of Polyamide 6 has been evaluated using the MD simulations and quantum
vibrational calculations.[102] The combined
theoretical approach has been successfully applied for the analysis
of the hydration structures of the title compound. We conclude that
the combined experimental and theoretical techniques provide significant
insights into the spectroscopic manifestation of strong solute–water
interactions and the structure of the hydration shell of bioactive
molecules.
Conclusions
The classical MD simulations
used in combination with the DFT computations
in the microsolvation limit demonstrate a specificcharacteristic
of the hydration shell structure of the carboxylate (−CO2–) group in the diclofenac anion. It is
an eight-atom ring formed by two water molecules, and the −CO2– group linked by three intermolecular H-bonds
(the R33(8) motif). The motif is generated by
steric hindrance resulting from the structure of diclofenac anion
(the intramolecular N–H···O bond, etc.). Overtones
of wagging vibrations in water molecules, which form the eight-atom
ring, superpose the bending vibration of the water molecule, which
forms the shortest H-bond with the −CO2– group. As a result of Fermi resonance, a deep hole is found in the
ATR-IR spectrum of the aqueous solution of sodium diclofenac at approximately
1750 cm–1. We attribute this to the relatively strong
specific interaction of water with the steric hindrance −CO2– group.Screening of the Cambridge
Structure Database shows that the R33(8) motif
occurs in solvates and co-crystals of
pharmaceutical compounds, which contain the steric hindrance −CO2– group. We do hope that the methodology
developed for theoretical analysis of ATR-IR spectra could provide
a model for further IR/Raman studies of the strong interaction between
the steric hindrance −CO2– group
of bioactive molecules and water molecules in dilute aqueous solutions.
Experimental Section
ATR-IR spectra were recorded with
a Nicolet 6700 infrared Fourier
spectrometer equipped with an attachment (Patent U.S. 5,172,182) with
a zinc selenidecrystal—single-reflection ATR accessory. The
IR spectra were detected in the 550–3500 cm–1 range with the resolution of 8 cm–1. The concentration
of the aqueous solution of NaDN varies from 0.4 to 0.02%. Each sample
was measured in triplicate, with each measurement repeated five times.
The choice of the upper concentration was determined by the following
reasons. First, at concentrations close to the solubility limit, the
dissolution was frequently incomplete, which could have led to a distortion
of the spectrum due to sample inhomogeneity. Second, the problem with
incorrect comparisons of spectra with substantially different concentrations
might be due to differences in the refractive indexes. At the target
concentrations, the refractive indexes were almost identical between
experimental samples and as compared with the refractive index of
water.The measurement procedure details are given in the corresponding
paragraph of the Supporting Information.
Computational Methods
Molecular
Dynamics Simulations
The
GROMACS code[103−106] was used to perform the MD simulations. The MD simulations were
performed for two systems corresponding to available experimental
concentrations.[107] The first one included
1 molecule of NaDN and 4400 water molecules (∼0.4%) placed
in a cubiccell. The other used 1 molecule of NaDN and 1000 water
molecules (∼1.7%) placed in cubiccell. For NaDN, the potentials
based on the parameters of the force field OPLS-AA[108] were used together with the SPC/E water model.[109] Atomic partial charges and van der Waals parameters
of DN anion are given in Table S1 of the
Supporting Information. The simulations were carried out in the NVT (constant number, constant volume, and constant temperature)
ensemble. The volumes of cubiccells were chosen according to experimental
densities of 1.7 and 0.4% aqueous solutions of sodium diclofenac (1.00475
and 1.00040 g mL–1, respectively). The temperature
maintained at 298 K employing the velocity-rescaling temperature coupling[110] with the time constant of 0.5 ps. The equations
of motion were integrated using the leap-frog algorithm[111] with a time step of 0.5 fs. Long-range electrostatic
interactions were calculated using the particle mesh Ewald method[112,113] (the cutoffs were set at 15 Å for ∼1.7% solution modeling
and 25 Å for ∼0.4% solution); van der Waals and short-range
interactions were truncated at 14 Å for ∼1.7% solution
and 24 Å for ∼0.4% solution. The fluctuations of kinetic,
potential, and total energy around some mean values serve as a criterion
of the equilibration of the systems. For information purposes, 10
ns (a time step was 0.5 fs) simulations were performed.
DFT Computations
The structure and
IR spectrum of the DN– anion and its complexes with nH2O molecules, DN–·nH2O, where n varies from 0
to 5, were computed at the B3LYP/6-311++G** level using Gaussian 03
software package.[114] This level of approximation
is efficiently used to establish a relation between experimental spectra
and the underlying conformations of bioactive compounds in the microsolvation
limit.[51] The scaled factors[115] have not been used for harmonic frequencies.
The starting structures of complexes with a particular n were borrowed from the literature.[65] London
dispersion interactions were taken into account by using the B97D/6-311++G**
approximation.[116] In accord with the literature
data,[117,118] these interactions were found to have little
influence on the geometrical and IR spectroscopic parameters of intermolecular
H-bonds in the target/analyzed complexes.The energy of Ow–H···Cl and H2Ow···Cl noncovalent interactions Eint was evaluated by the Bader analysis of electron density[119] in conjunction with the Espinosa scheme[120]where Gb is the
local electronic kinetic energy density at the Ow–H···Cl
or H2Ow···Cl bond critical point
in electron density.[121]Equation yields reasonable Eint values for Cl···Cl and Hal···O
noncovalent interactions, where Hal = F or Cl, in gas and condensed
phases.[122−124]
Authors: B Koeppe; S A Pylaeva; C Allolio; D Sebastiani; E T J Nibbering; G S Denisov; H-H Limbach; P M Tolstoy Journal: Phys Chem Chem Phys Date: 2017-01-04 Impact factor: 3.676