Modeling the intermolecular interactions: Molecular structure of N-3-hydroxyphenyl-4-methoxybenzamide

Article abstract of DOI:10.1016/j.jmgm.2013.11.001

The title compound, N-3-hydroxyphenyl-4-methoxybenzamide (3) was prepared by the acylation reaction of 3-aminophenol (1) and 4-metoxybenzoylchloride (2) in THF and characterized by ¹H NMR, ¹³C NMR and elemental analysis. Molecular structure of the crystal was determined by single crystal X-ray diffraction and DFT calculations. 3 crystallizes in monoclinic P2 ₁/c space group. The influence of intermolecular interactions (dimerization and crystal packing) on molecular geometry has been evaluated by calculations performed for three different models; monomer (3), dimer (4) and dimer with added unit cell contacts (5). Molecular structure of 3, 4 and 5 was optimized by applying B3LYP method with 6-31G+(d,p) basis set in gas phase and compared with X-ray crystallographic data including bond lengths, bond angles and selected dihedral angles. It has been concluded that although the crystal packing and dimerization have a minor effect on bond lengths and angles, however, these interactions are important for the dihedral angles and the rotational conformation of aromatic rings.

Full text of DOI:10.1016/j.jmgm.2013.11.001

Accepted Manuscript
Title: Modeling the Intermolecular Interactions: Molecular
Structure of N-3-hydroxyphenyl-4-methoxybenzamide
Author: Sedat Karabulut Hilmi Namli Raif Kurtaran Leyla
Tatar Yildirim Jerzy Leszczynski
PII:
S1093-3263(13)00197-6
DOI:
Reference:
http://dx.doi.org/doi:10.1016/j.jmgm.2013.11.001
JMG 6355
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Journal of Molecular Graphics and Modelling
Received date:
Revised date:
Accepted date:
11-7-2013
2-11-2013
16-11-2013
Please cite this article as: S. Karabulut, H. Namli, R. Kurtaran, L.T. Yildirim, J.
Leszczynski, Modeling the Intermolecular Interactions: Molecular Structure of N-3-
hydroxyphenyl-4-methoxybenzamide, Journal of Molecular Graphics and Modelling
(2013), http://dx.doi.org/10.1016/j.jmgm.2013.11.001
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Modeling the Intermolecular Interactions: Molecular
Structure of N-3-hydroxyphenyl-4-methoxybenzamide
Sedat KARABULUT a*, Hilmi NAMLI a, Raif KURTARAN b, Leyla TATAR YILDIRIMc
and Jerzy LESZCZYNSKId
aBalıkesir University, Faculty of Science and Literature, Department of Chemistry, 10145
Cagis, Balikesir, Turkey
bAkdeniz University, Alanya Faculty of Engineering, Materials Science and Engineering
Antalya, Turkey
cHacettepe University, Department of Engineering Physics, Beytepe, 06800 Ankara, Turkey
dJackson State Univ., Interdisciplinary Nanotoxicology Ctr., Jackson, MS, USA
ABSTRACT
The title compound, N-3-hydroxyphenyl-4-methoxybenzamide (3) was prepared by
the acylation reaction of 3-aminophenol (1) and 4-metoxybenzoylchloride (2) in THF and
1
characterized by H-NMR, 13C-NMR and elemental analysis. Molecular structure of the
crystal was determined by single crystal X-ray diffraction and DFT calculations. 3 crystallizes
in monoclinic
space group. The influence of intermolecular interactions (dimerization
P 21 / c
and crystal packing) on molecular geometry has been evaluated by calculations performed for
three different models; monomer (3), dimer (4) and dimer with added unit cell contacts (5).
Molecular structure of 3, 4 and 5 were optimized by applying B3LYP method with 6-
31G+(d,p) basis set in gas phase and compared with X-ray crystallographic data including
bond lengths, bond angles and selected dihedral angles. It has been concluded that although
the crystal packing and dimerization have a minor effect on bond lengths and angles,
however, these interactions are important for the dihedral angles and the rotational
conformation of aromatic rings.
Keywords: Molecular Structure, Dimer, Amide, X-Ray, DFT.
* Corresponding author: Sedat Karabulut
e-mail: sedatk@balikesir.edu.tr
Telephone: +902666121000-1116
Fax: +902666121215
Page 1 of 30

INTRODUCTION
The amide group always remains in the center of interest to scientists because of large
variety of applications associated with compounds with such functional groups. Its presence
in molecules may render them the property of efficient complexing agents, effective
herbicides, in addition to importance of the amide fragment as the vital part of biomolecules
[1].
The physical properties of –NH-CO- functional group have attracted attention of many
experimental and theoretical scientists [2]. In addition to physical properties, also
conformational properties of –NH-CO- group have been studied extensively. For example,
formamide and substituted amides have been detected as planar species in both gas phase and
solid state [3-9]. However, there are also some experimental results that report small
deviations from planarity of amide functional group [6].
There are several applications of aromatic amide derivatives in crystal engineering
[10] because of the very active participating properties (electron charge distribution, non-
vanishing electrostatic multipole moment, magnetic ring current) of aromatic compounds in
numerous interactions [11]. Nature of substituent generally affects the molecular geometry,
reactivity, physicochemical and biological properties of aromatic compounds [12-14]. Based
on the resonance or inductive effects of substituents they can be either classified as electron-
donor or acceptor.
It is well known that hydrogen bonds are among interactions which are mostly
responsible for arrangement of molecules in crystal structure [15]. Thus the molecular
structures of aromatic amides should be well analyzed because of their diversity caused by
hydrogen bonding capacity. Hydrogen bonding is one of the most important non-covalent
interactions in the nature. The most famous examples of effects of hydrogen bonding on
Page 2 of 30

various species include property of water in different phases, structures and characteristics of
proteins and nucleic acids [16].
The molecular geometry of a dimeric amide structure basically depends on three main
factors; i) the molecular properties of the molecule itself (stereochemical and stereoelectronic
effects), ii) effect of dimerization, iii) crystal packing effects [17, 18].
The title compound (Figure 1) is an example of hydrogen bonded dimeric amide. As
the result of a crystallization process millions of molecules are gather together into unique
ordered arrangement. This arrangement is repeatable, under the same crystallization
conditions [19].
Figure 1
In the present work experimental study has been complemented by computational
approach. The geometric parameters of the title compound were calculated using following
input files: a monomer (3), a dimer (4), and a unit cell linked dimer (5). The monomer part of
all optimized molecular geometries (Figure 2) was compared with the analogous monomer
part obtained from the X-ray crystallographic data. Bond lengths, bond angles and dihedral
angles from experiment were compared with the predicted parameters. This comparison
identifies the key driving force that governs the molecular geometry of N-3-hydroxyphenyl-4-
methoxybenzamide monomer. The comparison of optimized monomer structure with
experimental X-ray data provided the effect of internal dynamics of N-3-hydroxyphenyl-4-
methoxybenzamide (substituents, stereochemical and stereoelectronic effects), the dimer
structure calculation is for the investigation of the effect of dimerization on molecular
geometry and the input file which has been constituted by definition of unit cell contacts is to
understand the effect of crystal packing on molecular geometry. If dimerization and crystal
packing are characteristic factors on the geometry of the title molecule, the regression
between the calculated geometric parameters of 4 and 5 v.s experimental X-ray data should be
better than 3. The aim of this study was to make a complete theoretical and experimental
structure analysis and identify the effective forces influencing the molecular geometry of title
compound by using the experimental X-ray data as reference.
Figure 2
Page 3 of 30

2. Materials and Methods
2.1. Material: 3-aminophenol, 4-methoxybenzoylchloride, Et3N, and THF were all
purchased from Fluka and used without further purification.
2.2. Physical Measurements: The elemental analyses were carried out at the
Eurovector 3018 CHNS analyzer. The NMR measurements were carried out at the BRUKER
DPX-400 FT-NMR Spectrometer. Perkin Elmer 1600 BX 2 FT-IR Spectrophotometer was
used for FT-IR analysis.
2.3. Synthesis: N-3-hydroxyphenyl-4-methoxybenzamide was prepared according to
the reported method [20]. 4-methoxybenzoilchloride (2.7 ml, 0.02 mol) and 3-aminophenol
(0.22 g, 0.02 mol) were dissolved and mixed in THF (30 ml). Three ethylamines (1.5 ml, 0.02
mol) were added dropwise to the mixture. The solution was stirred 15 hours in ambient
temperature and the white precipitate filtered. 70 ml water was added to the filtrate and the
precipitate (product) filtered. The product was crystallized in the mixture of acetonitrile and
methanol (5:1), m.p: 233-234 0C. 1H-NMR (DMSO) δ ppm: 7.3 (1H, s, H2); 9.3 (1H, e, H1);
6.5 (1H, d, H4); 7.1 (1H, t, H5); 7.2 (1H, d, H6); 9.9 (1H, e, H); 7.9 (2H, d, H9, H13); 6.9
13
(2H, d, H10, H12); 3.8 (3H, s, H14A, H14B, H14C) (Figure 3). C-NMR (DMSO) δ ppm:
111 (C6), 108 (C5), 112 (C4), 132 (C3), 114 (C2), 130 (C1), 165 (C7), 162 (C8), 141 (C9,
C13), 128 (C10, C12), 158 (C11), 55 (C14) (Figure 3). Elemental Analysis: %69.55 C,
%5.69 H, %6.13 N.
Figure 3
2.4. Infrared Spectrum: The FT-IR spectrum of reagents and the product was recorded
at solid state with KBr pellet technique and overlaid for comparison (Figure 4).
Figure 4
2.5. X-ray Diffraction Structure Analysis: X-ray diffraction measurements were
performed with CuKα (λ=1.54184 Å) radiation on an Enraf-Nonius CAD4 (κ-geometry)
Page 4 of 30

diffractometer, operating in ω/2θ scan mode, equipped with a graphite-monochromated. The
lattice parameters and their estimated standard deviations were determined from a least-
squares refinement of 20 centred reflections in the range of 21.49°≤θ≤ 42.30° by using CAD4
Express [21]. During data collection, three standard reflections that were periodically
measured every 120 minutes showed no significant intensity variation. A total of 4800
reflections were collected in the range 3.43°≤θ≤74.18°, of which 4606 independent reflections
were used for the structure determination. Data reduction was carried out using XCAD4 [22].
The structure was solved by direct methods and refined using the programs SHELXS97 and
SHELXL97 [23], respectively, in the WinGX package [24]. A full-matrix least-squares
refinement on F2 converged at R = 0.0642. Atomic scattering factors were taken from the
International Tables for X-ray Crystallography [25]. Hydrogen atoms of the OH and NH
groups were taken from a difference Fourier map and fixed. The hydrogen atoms of phenyl
and methyl groups were placed with Uiso(H)=1.2 Ueq(C) and Uiso(H)=1.5 Ueq(C), respectively.
For all non-hydrogen atoms anisotropic displacement parameters were refined. Table 1 shows
the crystal data and details of crystal refinement; Table 2 shows the atomic coordinates and
equivalent isotropic displacement parameters. The ORTEP [26] drawing of the molecule is
shown in Figure 5. Hydrogen bond and molecular packing geometry of the title molecule
were calculated with PLATON [27, 28] and hydrogen bonding geometry is summarized in
Table 3.
Table 1
Table 2
Figure 5
Table 3
2.6. Computational Details: Gaussian 03 [29] software was used for all calculations.
Input files for monomer (3) and H-bonded dimer (4) was prepared based on experimental X-
ray structure. However, the experimental data were modified for the unit cell linked structure
(5), due to high computational expenses of the optimization of a complete crystal packing
structure. In this modified input the HO- linkages were replaced by water and the HN-
replaced by ammonia (Figure 6). All structures were optimized at the B3LYP/6-31G+(d, p)
[30, 31] level. Vibrational frequency calculations have been performed after optimization and
Page 5 of 30

no imaginary frequencies were detected. Optimized results were compared with X-Ray
crystallographic data using bond lengths, bond angles, and selected dihedral angles which are
responsible from the gauche conformation (Figure 7) of aromatic rings.
Figure 6
Figure 7
The input file of monomer has been generated by selecting the minimum energy
geometry from three dimensional potential energy surfaces (C1-N, C8-C7 and energy) of the
monomer which were calculated at semiemprical AM1 level [32].
Dimerization energy at B3LYP 6-31+G(d, p) level was calculated as 15 kcal/mol.
Basis set superposition error has been considered at three basis sets levels (6-31+G(d, p), 6-
311+G(d,p) and 6-311++G(2d,2p)). It has been concluded that there is no remarkable
difference between the counterpoise corrections which has been calculated at different levels.
3. Result and Discussion:
There are two types of H-bonds in the crystal structure of the title compound: C=O---
H-O and N-H---O-H (Figure 3). Former are used for the dimerization and the latter connect
the unit cells to build up the crystal structure. However, though the nitrogen electron lone
pairs are better electron donor than the oxygen, they have no role in hydrogen bonding for this
crystal packing system (Figure 3). One of the main reason of this situation is the interaction of
nitrogen lone pairs with carbonyl π* orbital. Figure 8 shows the calculated HOMO of the title
molecule. HOMO is generally located on one of the aromatic ring and nitrogen atom, due to
the electron donating properties of –OH and –NH - and nitrogen lone pair electrons. As it can
be seen from the orbital diagram (Figure 8) lone pairs of nitrogen are delocalized to the
carbonyl π* which explains why the lone pairs are not used to form intermolecular hydrogen
bonds.
Figure 8
Page 6 of 30

The crystal-packing have been structurally characterized by the single crystal X-ray
crystallography. Single crystal X-ray diffraction analysis of prismatic-colorless crystal shows
the crystallization in monoclinic system with space group P21/c. and cell constants are: a =
13.167(3), b =11.880(3), c =15.830(8) Å, β = 101.92(3)°.
X-H...Cg (π-ring) interactions were calculated using the PLATON software. Two
closest near X-H...Cg interactions between asymmetric units have been identified. Planes of
π-rings include Cg1: C8–C9–C10–C11–C12–C13 and Cg2: C8′–C9′– C10′–C11′–C12′–C13′,
atoms, where the Cg refers to the ring centre of gravity. [Cg1=0.64190(12), 0.31078(16),
0.32520(12), Cg2=-0.14932(14), 0.94010(16), 0.16920(12)]. Details of the closest near X-
H…π-ring interactions are given Table 4.
Table 4
The formation of amides by the reaction of amines and acylchlorides is a favorable
reaction and the synthesis was completed without any heating of the reactants. The product
has been successfully synthesized and purified by crystallization. The absence of the double
absorption bands at 3360 cm-1 (symmetric and asymmetric stretching of amine functional
group) and 1768 cm-1 (carbonyl stretching) at the spectrum of product (Figure 4 c) is one of
the indications of the formation of amide functional group. The carbonyl stretching band at
1608 cm-1 represents another proof of successful synthesis. The results of NMR and elemental
analysis are also consistent with the molecular structure of the obtained compound.
The hydrogen bond and covalent bond lengths of experimental X-ray structure have
been compared with calculated bond lengths. The data displayed in the Table 5 indicate that
the hydrogen bonds of the dimer model (4) and unit cell contacted model (5) are almost
identical, and both are shorter than the experimental results. Crystal structure effects may be
suggested as one of the reasons for the difference between experimental and theoretical
results.
Table 5
Regression analysis has been carried out for calculated bond lengths and R2 values
obtained using the experimental X-ray bond lengths as a reference. R2 values are 0.96, 0.97,
Page 7 of 30

0.97 for monomer, dimer, and crystal pack optimized structures, respectively. Although R2
values are similar, the sum of differences between experimental and calculated bond lengths
(∑ Absolute (Exp. Bond Length-Calc. Bond Length)) have also been analyzed for a complete
comparison (Table 6).
Table 6
Interestingly, the sum of absolute bond length differences is quiet similar to the
determined coefficients (R2). Thus, it can be suggested that the dimerization and crystal
packing have no significant effect on bond lengths of title molecule.
The effect of dimerization and crystal packing on the bond angles is similar to their
effect on bond length when the distribution coefficients of bond angles are considered. The R2
value is around 0.80 for all fitting graphics of bond angles (Figure 9). As mentioned before
there is another parameter to evaluate the consistency of calculated values - sum of absolute
differences. The sum of absolute differences was computed as 65.6, 60.9 and 62.4 for
monomer, dimer, and crystal packing models, respectively. When these values are taken into
account, the dimer structure represents the closest model to the X-ray results. However, the
differences among all predicted models are not significant. Therefore, it can be concluded that
intermolecular interactions (dimerization and crystal packing) do not considerably effect on
bond angles and bond lengths of the title molecule.
Figure 9
Some of the dihedral angles were not considered in the analysis because of fixed
aromatic rings. However, rotatable dihedral angles were selected (Table 7) because of their
remarkable effect on conformation. Selected experimental and theoretical dihedral angles
were compared using the same methodology as described above. Though the R2 values
calculated are similar (Figure 10), as those obtained in the bond length and angle comparison,
however, the sum of calculated dihedral angles is considerably different (Table 7). As it can
be deducted from the data in Table 7, dimerization and crystal packing especially affect two
dihedrals (C13-C8-C7-N and C13-C8-C7-O2). These two dihedral angles characterize the
position of methoxy substituted aromatic ring and amide functional group. It is clear that the
Page 8 of 30

rotational preference of the C8-C7 bond is strongly affected by dimerization and
crystallization.
Table 7
Figure 10
This conclusion allows hypothesizing about the mechanism of crystallization of title
molecule. Almost planar configuration (related to the arrangement of two aromatic ring and
amide functional group) of the N-3-hydroxymethyl-4-methoxy benzamide monomer can be
assumed. The first hydrogen bond is formed between H1 and O2. Then the C8-C7 bond
rotates, to adopt the best position facilitating the formation of the second hydrogen bond (H1’-
O2). Consequently, the dimer is formed (Figure 11).
Figure 11
The binding energy has been calculated 15 kcal/mol and this energy may be supplied
for the rotation of C8-C7 bond to connect monomers at best fitting geometry and build the
crystal structure.
4. Conclusion
The goal of study is to explain the effect of various interactions governing molecular
structure of title compound. The optimized monomer structure (3) represents the pristine,
structural properties (stereochemical and stereoelectronical) of the compound. The dimer
structure (4) additionally includes effect of dimerization. The last step, crystal packing
optimization (5) covers also the effect of crystal packing. Obtained results showed that the
bond lengths and bond angles are not affected by dimerisation and crystal packing. Contrary
to bond angles and lengths, some of dihedral angles are highly depended on dimerization and
crystal packing. From the obtained results it can be concluded that the studied kind of
molecules form the crystal by arranging the dihedral angles to the most suitable position. Thus
the crystal structures can be different from the monomer structures in solution, especially
when dihedral angles are considered.
Acknowledgements
Page 9 of 30

The authors acknowledge the Balikesir University, Hacettepe University and Jackson
State University for the provided facilities for computational and experimental works.
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FIGURE CAPTIONS
Figure 1: Synthesis, dimerization and crystal packing of N-3-hydroxyphenyl-4-
methoxybenzamide.
Figure 2: Monomer (a), dimer (b) and dimer with unitcell contacts (c) input models.
Highlighted parts were compared with the experimental X-Ray results.
Figure 3: Crystal structure of N-3-hydroxyphenyl-4-methoxybenzamide and labeling
of atoms.
Figure 4: The overlaid FT-IR spectra of the reagents (3-aminophenol and 4-
methoxybenzoilchloride), and the product (N-3hydoxyphenyl-4-methoxybenzamide).
Page 11 of 30

Figure 5: ORTEP drawings of asymmetric units of N-3-hydroxyphenyl-4-
methoxybenzamide
Figure 6: Ammonia and water unit cell linkage model.
Figure 7: Gauche conformation of two aromatic rings of N-3-hydroxyphenyl-4-
methoxybenzamide.
Figure 8: HOMO of N-3-hydroxyphenyl-4-methoxybenzamide (isovalue=0.02).
Figure 9: Fitting graphics and determination coefficients of calculated bond angles for
monomer (a), dimer (b) and crystal pack (c) models with experimental X-Ray reference.
Figure 10: Fitting graphics and determination coefficients of calculated dihedral
angles for monomer (a), dimer (b) and crystal pack (c) models with experimental X-Ray
reference.
Figure 11: Dimerisation steps of N-3-hydroxyphenyl-4-metoxybenzamide.
Page 12 of 30

Table 1. Crystal data and experimental details of the title compound
Empirical formula
C14 H13 N O3
Formula weight
Crystal system
Space group
243.25
Monoclinic
P 21/c
Crystal shape /color
Prism/colorless
2422.8(15)
Volume (Å3)
Z
8
Dcalc (Mg/m3)
Absorbtion coefficient (mm-1)
F(000)
1.334
0.777
1024
h, k, l ranges
0→ 16, -14 →0, -19 →19
Refinement on F2
2
2
2
,
⎤
⎡
w =1 σ F +(0.1395P)
0
⎣
⎦
P = (F02 + 2Fc2 )/3
Reflections collected/unique
Parameters
4800/4606 [Rint=0.0642]
326
0.976
R1= 0.0807, wR2= 0.1983
R1= 0.1831, wR2= 0.2562
Goodness of fit on F2
R indices [I>2σ(I)]
R indices [all data]
Largest difference peak and hole 0.538 and -0.269
(e/Å3)
Additional material available from Cambridge Crystallographic Data Center as deposition
numbers: CCDC 934952.
Page 13 of 30

Table 2. Atomic coordinates and equivalent isotropic displacement parameters
for non-hydrogen atoms of two asymmetric units of the compound.
Ueq = (1 )
U a*a*a a
ij i j i j
3
∑i ∑j
Atom
x
y
z
Ueq (Å2)
N
0.3808(3)
0.02501(19)
0.3936(2)
0.8450(2)
0.2778(3)
0.2032(3)
0.1025(3)
0.0762(3)
0.1512(4)
0.2532(3)
0.4327(3)
0.5406(3)
0.5696(3)
0.6703(3)
0.7424(3)
0.7143(3)
0.6142(3)
0.8791(4)
0.3566(3)
0.2237(2)
0.1764(3)
0.3341(3)
0.3550(3)
0.2838(3)
0.2892(3)
0.3608(4)
0.4314(4)
0.4294(4)
0.2715(4)
0.2939(3)
0.3941(4)
0.4105(4)
0.3288(4)
0.2282(4)
0.2092(4)
0.4339(4)
0.1877(2)
0.13203(18) 0.0495(8)
0.0479(9)
O1
O2
O3
C1
C2
C3
C4
C5
C6
C7
0.2351(2)
0.4093(2)
0.1389(3)
0.1597(3)
0.1112(3)
0.0423(3)
0.0224(3)
0.0710(3)
0.2335(3)
0.2803(3)
0.3240(3)
0.3687(3)
0.3685(3)
0.3265(3)
0.2832(3)
0.4561(3)
0.0620(9)
0.0693(10)
0.0398(10)
0.0398(9)
0.0418(10)
0.0590(13)
0.0675(15)
0.0596(13)
0.0441(10)
0.0422(10)
0.0484(10)
0.0522(11)
0.0480(11)
0.0505(11)
0.0483(11)
0.0788(18)
C8
C9
C10
C11
C12
C13
C14
N'
0.1110(2)
0.4680(2)
0.0978(2)
-0.3506(2)
0.2163(3)
0.2905(3)
0.3918(3)
0.4199(3)
0.3461(4)
0.2440(3)
0.0585(3)
-0.0491(3)
-0.0763(4)
-0.1035(3)
0.0273(2)
0.0763(2)
-0.0828(3)
-0.1023(3)
-0.0309(3)
-0.0402(3)
-0.1196(4)
-0.1909(4)
-0.1850(4)
-0.0186(4)
-0.0423(3)
-0.1420(4)
-0.1610(4)
-0.0784(4)
0.0226(4)
0.0417(4)
-0.1814(5)
0.3081(2)
0.35710(18) 0.0480(8)
0.0416(8)
O1'
O2'
O3'
C1'
C2'
C3'
C4'
C5'
C6'
C7'
C8'
C9'
0.2570(2)
0.0792(2)
0.3537(2)
0.3337(3)
0.3776(2)
0.4410(3)
0.4602(3)
0.4163(3)
0.2620(3)
0.2154(3)
0.1723(3)
0.1250(3)
0.1235(3)
0.1667(3)
0.2122(3)
0.0300(4)
0.0571(9)
0.0776(11)
0.0367(9)
0.0406(9)
0.0399(9)
0.0497(11)
0.0530(12)
0.0488(11)
0.0431(10)
0.0413(10)
0.0528(11)
0.0579(13)
0.0511(12)
0.0521(12)
0.0464(11)
0.095(2)
C10' -0.1765(4)
C11' -0.2486(3)
C12' -0.2226(3)
C13' -0.1227(3)
C14' -0.3808(5)
Page 14 of 30

Table 3. Details of hydrogen bonds between donor (D), acceptor (A) and hydrogen (H).
D − H ⋅⋅⋅ A
N – H⋅⋅⋅O1′i
D−H (Å) A⋅⋅⋅H (Å)
D⋅⋅⋅A (Å) D−H⋅⋅⋅H (Å)
0.86
0.87
1.01
1.11
0.93
0.93
2.17
2.14
1.66
1.56
2.33
2.33
3.026(5)
3.004(4)
2.668(4)
2.654(4)
2.846(5)
2.874(5)
172
174
175
167
114
117
N′ – H′⋅⋅⋅O1ii
O1 – H1⋅⋅⋅O2′iii
O1′ – H1′⋅⋅⋅O2iv
C2 – H2⋅⋅⋅O2
C2′ – H2′⋅⋅⋅O2′
Symmetry codes [i= 1-x,-1/2+y,1/2-z ; ii = -x,1/2+y,1/2-z ; iii= x,-1+y,z ; iv= x,1+y,z]
Table 4: The distance between the closest near X-H---π-ring surface.
X − H ⋅⋅⋅ π
H−π (Å) C - π (Å) X - H⋅⋅⋅π (°)
C5′ – H5′⋅⋅⋅Cg1a
2.84
3.657(5)
147
C14 – H14C⋅⋅⋅Cg2b
2.98
3.779(5)
141
Symmetry codes [a= 1-x, 1-y, 1-z ; b=1+x,3/2-y,1/2+z ]
Table 5: Experimental and theoretical hydrogen bond distances.
Experimental
Dimer (4) (Å) Dimer with unit cell (5) (Å)
X-Ray (Å)
1.81
1.75
1.76
1.73
1.74
O2′---H1
O2---H1′
1.84
Page 15 of 30

Table 6: Experimental (X-Ray), Theoretical (Monomer, Dimer, Crystal Pack) bond lengths
(Å) and absolute differences between experimental and theoretical values.
Theo.
Crystal
Pack
Absolute
(Xray-
Mon.)
Absolute
(Xray-
Dim.)
Absolute
(Xray-Cry.
Pack)
Experimental
X-Ray
Theo.
Monomer Dimer
Theo.
Atom1 Atom2
H1
H
O1
N
H2
H9
H13
H10
H4
H6
H5
H12
H14A
H14B
H14C
C7
C7
C4
C11
C10
C5
C3
C13
C3
C11
C6
C9
C10
C1
C5
C13
C14
C1
0.87
0.91
0.93
0.93
0.93
0.93
0.93
0.93
0.93
0.93
0.96
0.96
0.96
1.25
1.35
1.37
1.37
1.37
1.37
1.38
1.38
1.38
1.38
1.39
1.39
1.39
1.39
1.40
1.40
1.42
1.42
1.48
0.97
1.01
1.08
1.09
1.08
1.08
1.08
1.09
1.09
1.09
1.10
1.09
1.10
1.23
1.36
1.38
1.36
1.40
1.39
1.37
1.39
1.40
1.41
1.41
1.40
1.40
1.40
1.39
1.41
1.42
1.41
1.50
0.99
1.01
1.08
1.09
1.08
1.08
1.08
1.09
1.09
1.08
1.10
1.09
1.10
1.24
1.37
1.40
1.36
1.40
1.39
1.35
1.39
1.40
1.41
1.40
1.40
1.40
1.40
1.39
1.41
1.42
1.42
1.50
0.99
1.02
1.08
1.09
1.09
1.08
1.08
1.09
1.09
1.08
1.10
1.09
1.10
1.24
1.36
1.40
1.36
1.40
1.39
1.36
1.39
1.40
1.40
1.41
1.40
1.40
1.40
1.39
1.41
1.42
1.42
1.50
0.10
0.10
0.15
0.16
0.15
0.15
0.15
0.16
0.16
0.15
0.14
0.13
0.14
0.01
0.01
0.01
0.01
0.03
0.02
0.01
0.01
0.02
0.02
0.02
0.01
0.01
0.01
0.00
0.01
0.01
0.01
0.02
0.12
0.10
0.15
0.16
0.15
0.15
0.15
0.16
0.16
0.15
0.14
0.13
0.14
0.00
0.02
0.03
0.01
0.03
0.02
0.02
0.01
0.02
0.02
0.02
0.02
0.01
0.01
0.00
0.01
0.01
0.00
0.02
0.12
0.11
0.15
0.16
0.16
0.15
0.15
0.16
0.16
0.15
0.14
0.13
0.14
0.00
0.01
0.03
0.01
0.03
0.02
0.02
0.01
0.02
0.02
0.02
0.01
0.01
0.01
0.00
0.01
0.01
0.00
0.02
C2
C9
C13
C10
C4
C6
C5
C12
C14
C14
C14
O2
N
C3
O3
C11
C4
O1
C12
C2
C12
C1
C8
C9
C2
C6
C8
O3
N
C8
C7
Sum of absolute bond length differences
2.10
2.14
2.15
Page 16 of 30

Table 7: Experimental and theoretical dihedral angles, sum of absolute differences of
theoretical and experimental dihedral angles (Å).
Monomer
Model
-177.2
3.5
Dimer
Model
-176.9
3.8
Crystal Pack
Model
Experimental
-179.5
2.5
C1-N-C7-C8
C1-N-C7-O2
-175.9
4.1
C13-C8-C7-N
C13-C8-C7-O2
C14-O3-C11-C10
-142.0
36.1
0.1
-157.3
22.0
-0.2
-150.0
29.4
0.5
-138.5
41.5
1.6
H1-O1-C3-C4
Sum of absolute
differences
168.7
179.7
179.0
178.8
43.9
29.3
25.7
Page 17 of 30

Figure1
Figure 1
Page 18 of 30

Figure2
Figure 2:
Page 19 of 30

Figure3
Figure 3:
Page 20 of 30

Figure4
Figure 4
Page 21 of 30

Figure5
Figure 5:
Page 22 of 30

Figure6
Figure 6:
Page 23 of 30

Figure7
Figure 7:
Page 24 of 30

Figure8
Figure 8:
Page 25 of 30

Figure9
Figure 9:
Page 26 of 30

Figure10
Figure 10:
a
b
c
Page 27 of 30

Figure11
Figure 11:
Page 28 of 30

Graphical Abstract (for review)
Page 29 of 30