Contribution of Directional Dihydrogen Interactions in the

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The Contribution of Directional Dihydrogen Interactions in the Supramolecular Assembly of Single Crystals: Quantum Chemical and Structural investigation of C17H17N3O2 Azine Leonardo R. Almeida, Paulo S. Carvalho Jr, Hamilton B. Napolitano, Solemar Silva Oliveira, Ademir J. Camargo, Andreza Figueredo, Gilberto Lucio Benedito de Aquino, and Valter Henrique Carvalho-Silva Cryst. Growth Des., Just Accepted Manuscript • DOI: 10.1021/acs.cgd.7b00585 • Publication Date (Web): 30 Aug 2017 Downloaded from http://pubs.acs.org on August 30, 2017

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Crystal Growth & Design

The

Contribution

of

Directional

Dihydrogen

Interactions in the Supramolecular Assembly of Single Crystals: Quantum Chemical and Structural investigation of C17H17N3O2 Azine Leonardo R. de Almeida§ , Paulo S. Carvalho-Jr*§, Hamilton B. Napolitano§, Solemar S. Oliveira§, Ademir J. Camargo§, Andreza S. Figueredo§, Gilberto L. B. de Aquino§ and Valter H. Carvalho-Silva.*§ §

Grupo de Química Teórica e Estrutural de Anápolis, Campus de Ciências Exatas e

Tecnológicas, Universidade Estadual de Goiás, Caixa Postal 459, 75001-970, Anápolis, GO, Brazil.

ABSTRACT

Crystalline systems can be organized from several types of intermolecular interactions, among which classical and weak H-bonds are the most common, playing a very important role in the supramolecular assembly. However, in recent years a number of works have considered the influence of the homonuclear dihydrogen interaction, which had been neglected for a long time, to describe the supramolecular assembly of single crystals. In the C17H17N3O2 azine of the

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present study, a non-classical dihydrogen interactions (C−H···H−C contact) have appeared in crystal structure with a fundamental contribution on the stability of crystalline packing. Nonetheless, an x-ray structural analysis is not conclusive to assess the real importance of the C−H···H−C contact.

In order to characterize the nature and implications of C–H ···H–C

contacts concomitant with the classical interactions, the crystallized compound was evaluated by Hirshfeld surface, QTAIM, NBO and Car-Parrinello Molecular Dynamics. The results establish that these interactions really exist and their extension is responsible for the cooperative effect on the stability of crystalline packing. We expect that a more thorough understanding and description of homonuclear dihydrogen interactions in the supramolecular assembly of C17H17N3O2 can assist in the crystal engineering of small molecules, offering a drive on physicalchemistry parameters of biological and material processes.

INTRODUCTION Chemical interactions are important issues in the biological,1–4 physical, catalytic,5,6 and chemical7 processes. Conventional hydrogen bonds (H-bonds) and weak interactions govern the molecular packing in solid-state. Although the nature of crystal is unpredictable, the understating of chemical interactions has been extensively applied to designing functional materials.4,8 In this context, conventional H-bonds, a bond bridging two electronegative atoms by an H atom, are well documented; however, weak interactions are relatively unexplored. Among them, weak interactions defined by H atom contacts between homopolar bonds,9 namely dihydrogen interactions,9–19 have been recognized as important supramolecular features in the assembly of molecules, notably those containing hydrophobic groups.14,20–22 Remarkably, the dihydrogen bond (DHB) term is designated just in the presence of polarized hydridic hydrogen (X-H, X=


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metal, N, O, B…); on the other hand, a homonuclear interaction has been termed as an H-H bond, H-H interaction, dihydrogen contact or dihydrogen interaction.14,23–25 The C−H···H−C moiety, configuring a chemical interaction, differs from a typical van der Waals contact both in energy and in geometry.23,26 Although the short H···H parameter (2.0−3.0 Å) has lower frequency in crystals,21,27 the accumulation of C−H···H−C contact is strong and directional enough to hold molecules in a crystal arrangement.28 Through diverse approaches, the topology and physical nature of the C−H···H−C contact in the molecular packing in crystals have been investigated.11,13,24,29–31 Noteworthy, it is the shortest C−H···H−C distance (1.566 Ǻ) reported by neutron diffraction of tri(3,5-tert-butylphenyl)methane. The stabilization and directionality of this contact was supported by the decisive energetic London dispersion contribution27. Structural parameters from quantum chemical calculations are particularly useful in the statement of these interactions and their influence on the physical properties of materials. Assisted by Quantum Theory of Atoms-in-Molecules (QTAIM)32,33 and Hirshfeld surface (HS)34 approaches; solid-state transition, colouring and fluorescent properties of 1-(anthracen-9-yl) pyrene polymorphs have been correlated with an increase in the extent of C−H···H−C contacts.35 Similarly,

these

contacts

have

provided

photophysical

properties

in

polyaromatic

hydrocarbons.36 Furthermore, the C−H···H−C contacts are fundamental in the comprehension of high melting points and vaporization enthalpies in alkanes.14,21 However, these contacts had been neglected for a long time in the literature, and it is only in recent years that several works37–39 have addressed this topic, especially with the contribution given by Echeverría.14,21,40,41 Based on these perspectives, a systematic study of dihydrogen interactions has become an important part of crystal engineering.


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Recently, the azines have been subjected to study because of the presence of functional weak and dihydrogen interactions.20,42–44 Azines are a class of organic compounds that exhibit R1C=N-N=CR2 (with R1 = or ≠ R2) connectivity.45 An appropriate substituent on R1 and R2 positions can lead to different applications.46 These compounds have presented a broad spectrum of biological activities, such as anticonvulsant, antibacterial, anti-inflammatory, antioxidant, and anti-tumoral.45,47–49 Also, due to their supramolecular versatility, azines can exhibit nonlinear optical and optoelectronic properties.50–53

In particular, the azo group (N=N) has shown

important features to increase the non-linear optical properties of azo-enaminone compounds.54– 57

In this work, a supramolecular solid-state description and quantum chemical study of the dihydrogen interactions of 1-[(E)-4-isopropylbenzilydene]-2-[(E)-4-nitrobenzylidene]-hydrazine (AZN) is reported (see Figure 1). This title compound is a typical azine in which the molecular skeleton is comprised of a hydrophobic isopropyl and a nitro substituent. This paper is organized with a structural description of AZN packing where the CH···HC interactions are identified. Then, from the quantum mechanical perspective, the nature and functionality of this interaction in the molecule assembly is explored. We conclude the work with a summary of our achievements.


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Figure 1. The molecular structure of AZN showing the atom-labelling scheme. Thermal ellipsoids drawn at the 50% probability level. The hydrogen atoms of the methyl group (C16) show a specific nomenclature. EXPERIMENTAL SECTION Synthesis and crystallization. 4-nitrobenzaldehyde (151.2 mg, 1.0 mmol) was dissolved in anhydrous ethanol (5 mL) and treated with a solution of 70% hydrazine monohydrate (1.0 mmol). The mixture was stirred at room temperature (25 °C) for ten minutes and then 4isopropylbenzaldehyde (149 mg, 1.0 mmol) was added. The reaction mixture was stirred for another 2 hours at room temperature (25 °C) and followed by TLC. The resultant precipitate was filtered and washed with cold ethanol to afford AZN as a yellow solid (162 mg, 0.55 mmol). Yield: 55 %. Melting point: 410.9 – 412 K. Single crystals of AZN suitable for X-ray analysis were grown by slow evaporation from methanol at room temperature. 1H NMR (500 MHz, CDCl3) δ: 1.28 (d, J= 6.9 Hz, 6H, CH3) 2.97 (hept, J= 6.9 Hz, 1H, CHCH3) 7.32 (d, 2H, J= 8.2 Hz, CHar.) 7.79 (d, 2H, J= 8.2 Hz CHar.) 8.00 (d, 2H, J= 8.7 Hz, CHar.) 8.29 (d, 2H, J= 8.7 Hz, CHar.) 8.66 (s, 1H, NCH) 8.69 (s, 1H, NCH), see SI. 13C NMR (125 MHz, CDCl3) δ: 23.7, 34.2, 123.5, 126.9, 128.6, 132.0, 144.2, 148.6, 152.7, 159.0, 162.1, see SI. IR (4000 – 500 cm-1): (NO2) 1520 and 1340 cm-1; (C=N) 1600 cm-1; (-CH (CH3)2) 2950 and 1375 cm-1, see SI. MS (m/z): [M+] 295; Fragments: 252; 176; 173; 91, see SI.


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Structural analysis. The single-crystal X-ray diffraction data for AZN were collected at 120(2) K (Cryostream, Oxford Cryosystems) on a Bruker D8 VENTURE diffractometer with a PHOTON 100 CMOS detector system equipped with a Mo INCOATEC IµS microfocus source (λ = 0.71073 Å. The cell refinement and data reduction were carried out also using the software SAINT.58 Using Olex2, the structure was solved by direct methods and the models obtained were refined by full–matrix least squares on F2 (SHELXTL59). The hydrogen atoms on the carbon atoms were positioned geometrically and refined using the riding model [C-H 0.93 Å with Uiso(H) = 1.2Ueq(C) for C sp2]. Molecular representation, tables and pictures were all generated by WingX,60 Olex2,61 ORTEP-3,60 MERCURY 3.662 programs. The Hirshfeld surfaces (HS) and their associated 2D fingerprint plots were carried out by means of Crystal Explorer 3.1.63,64 These analyses were used to investigate the intermolecular interactions in the crystal packing of AZN. The HS were generated on the basis of the normalized contact distances, which are defined in terms of di and de, relative to van der Waals radii of the atoms65–67. The resolution of dnorm surfaces was mapped over the colour scale ranging from −0.42 to 1.6 Å, with the fingerprint plots using the standard 0.6–2.6 Å view of de vs. di. The CIFs files of the AZN molecule collected at 120K were deposited in the Cambridge Structural Data Base under the codes CCDC 1489316 Copies of the data can be obtained, free of charge, via www.ccdc.cam.ac.uk. Molecular Dynamics. The ab initio Car-Parrinello Molecular Dynamics (CPMD) simulations were carried out employing the quantum ESPRESSO package.68 The electronic structure was investigated within the generalized gradient approximation to density functional theory (DFT), through the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional.69,70 Vanderbilt ultrasoft pseudopotentials71 were employed to represent core-valence electron


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interactions. A plane-wave basis set was used to expand the valence electronic wave function with an energy cutoff of 25 Ry. The equations of motion were integrated using the Verlet scheme with a time step of 5 au (0.121 fs), a total time of 21 ps and the wavefunction fictitious mass (µ) set to be 400 au. The boundary conditions and the NVT canonical ensemble were considered in the study. The temperature of the ionic system was controlled by the Nose-Hoover thermostats72 scheme to maintain the temperature around 300 K. In our simulations, we used a box under periodic boundary conditions of 10 x 10 x 50 Å dimensions with four molecules of C17H17N3O2 azine. These four molecules are representative of main interactions in the crystal packing. To access the evolution of CH⋅⋅⋅HC contact, , a simulation was performed in CH(CH3)2 and NO2 functional groups, keeping all the other atoms frozen. DFT Calculations. The geometry and atomic numbering used in the calculations are shown in Figure 1. Starting from X-ray structure, we optimized only the hydrogens atom positions of the systems of interest at M062X/6-311G(d,p) level.73 Density functional theory (DFT) energies were corrected employing a Petersson-Frisch empirical dispersion term.74 The interaction energies between azine molecules have been evaluated in several conformations: (i) A and B molecules as shown in Figure 2a - Eq. 1a, (ii) B and F molecules, Figure 2a - Eq. 1b, (iii) G and H molecules as in Figure 2b - Eq. 1c and (iv) between AB and CD dimers, Figure 2a - Eq. 2. The interaction energies have corrected by including basis set superposition error (BSSE) by the counterpoise method proposed by Boys and Bernardi.75

ࢤࡱ‫ۯ‬۰ = ࡱ‫ۯ‬۰ − ሺࡱ‫ ۯ‬+ ࡱ۰ ሻ

(1a)

ࢤࡱ۰۴ = ࡱ۰۴ − ሺࡱ۰ + ࡱ۴ ሻ

(1b)


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ࢤࡱ۵۶ = ࡱ۵۶ − ሺࡱ۵ + ࡱ۶ ሻ

(1c)

ࢤࡱ‫ۯ‬۰ି۱۲ = ࡱ‫ۯ‬۰ି۱۲ − ሺࡱ‫ۯ‬۰ + ࡱ۱۲ ሻ

(2)

In order to determine the torsion energy of the methyl group, a rigid scan of C17C-C15CC16C-HαC was performed at the M062X/6-311G(d,p) level, keeping the C17C atom frozen. The NBO analysis76–78 were performed to estimate the energy between the filled orbitals of one subsystem and the vacant orbitals of another one. The reason for doing this analysis is to obtain a measure of the intermolecular delocalization, also called hyperconjugation, which can be deduced from the second-order perturbation approach,

ࡱሺ૛ሻ = −࢔࣌

ࡲ૛࢏࢐ ࢤࡱ

(3)

where ‫ܨ‬௜௝ଶ is the Fock matrix element between the i and j NBO orbitals and ݊ఙ is the population of the donor orbital. NBO analysis was carried out at the M062X/6-311g(d,p) level of theory. All the quantum chemical calculations were carried out employing the Gaussian 09 program suite.79 The topological analyses32,33 were performed in terms of electron density (ρ), Laplacian of electron density (ᐁ 2ρ), Ellipticity of electron density (ߝ), Lagrangian kinetic energy density [G(r)], potential energy density [V(r)] and Energy density [E(r)] at the critical points (CP). A multiwfn program package80 was used to study the topological analysis of the electron density and bond order properties of the crystal structure. The interaction energy and the topological


8

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parameters have been also performed using the wB97XD81 and APFD82 functionals, starting from structures optimized at M062X/6-311G(d,p) level as inputs of calculations.

RESULTS AND DISCUSSION As previously stated, azine compounds have a structural versatility that results in a supramolecular diversity. From the crystal engineering and material designing perspectives, this topic assumes remarkable importance. To identify the influence of weak and non-conventional interactions in the crystal packing, crystal structures and DFT calculations of a p-nitro and pisopropyl substituted azine, AZN, was investigated. A detailed description of the AZN structure is depicted below. Table 1 exhibits the crystallographic data for this structure. The main intermolecular interactions for this compound are listed in Table S15 (Supporting Information). Figure 1 shows a view of the asymmetric unit of AZN. Table 1. Crystallographic information of the AZN collected at 120(2) K. Empirical formula

C17H17N3O2

Formula weight

295.33 g.mol-1

Temperature

120(2) K

Wavelength

MoKα 0.71073 Å

Crystal system

Triclinic

Space Group

ܲ1ത a = 7.074(6) Å

Unit cell dimensions

b = 8.108(7) Å c = 13.329(8) Å


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α = 95.469(4)° β = 104.295(4)° γ = 92.864(4)° Volume

735.46(2) Å3

Z

2

Calculated density (g.cm-3)

1.334 g.cm-3

Absorption coefficient

0.090 mm-1

F(000)

312.0

Crystal size

0.347 x 0.276 x 0.046 mm

θ range for data collection

5.062º to 51.612º

Limiting indices

-8 ≤ h ≤ 8, -9 ≤ k ≤ 9, -16 ≤ l ≤ 16

Reflections collected

18895

Reflections unique

2830 [Rint = 0.0854, Rsigma = 0.0549]

Data / restrictions / parameters

2830 / 0 / 201

Solution / refinement

Direct methods / least-square full matrix

Goodness-of-fit on F2

1.040

Final R indices [I>2σ(I)]

R1 = 0.0481; wR2 = 0.1124

R indices (All data)

R1 = 0.0764, wR2 = 0.1279

Largest diff. peak/hole / e Å-3

0.21/-0.34

Structural description. The AZN belongs to triclinic centrosymmetric ܲ1ത space group with a single molecule in the asymmetric unit, Z’ = 1 (Figure 1). As expected from the aromatic character of the C1=N2-N1=C8 moiety and ring groups, the central part of the molecule assumes a planar geometry with a dihedral angle of 6.29(2)º between the planes of the two phenyl rings. The C11−C12−C15−C17 and C11−C12−C15−C16 torsion angles are, respectively, 48.2(2)º and


10

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-76.36(2)°, which characterizes the orientation of the methyl groups with respect to the main molecular plane. Because AZN molecule is absence of conventional strong H-bonding donor groups, its packing is essentially featured only by non-conventional H-bonds. A view of the molecular packing of AZN along this direction is presented in Figure 2a. Along [010] direction AZN molecules are assembled by C16−H16A···O1 [dC16···O1 = 3.668(2) Å, 151.48°] and C16−H16A···O2 [dC16···O2 = 3.506(2) Å, 144.70°] to form a dimeric arrangement. This assembly is also stabilized by π···π interactions with centroid-centroid (Cg···Cg) distances of 3.988(2) Å. Along the [100] direction, these dimers are stacked into columns via additional π···π interactions [Cg2···Cg1 = 4.595(2) Å], as shown in Figure 2c. Also, adjacent dimers are connected each other by C16−H16C···O2 [dC16···O2 = 3.548(2) Å, 158.62°] and C11−H11···O2 [dC11···O12 = 3.584(2) Å, 157.68°]. The AZN molecules are arranged into layers along the [010] direction through C1−H1···O1 [dC1···O1 = 3.323(2) Å, 150.64°] and C7−H7···O1 [dC7···O1 = 3.514(2) Å, 142.25°] H-bonds, where the molecules are arranged in a head-to-tail fashion (Figure 2b). Thus, 2D assembly by C−H···O interaction is the key to allow the lateral arrangement through CH···HC contacts, establishing hydrophobic channels along the structure (highlighted in grey Figure 2a). It worth noting that in this region, the structure is stabilized mostly by long-range interactions and the H⋅⋅⋅H contacts. Since no intermolecular interactions are identified in this region, such contact assumes an importance in the packing of structure and the properties of lattice, e.g. m.p and solubility. In particular, the H⋅⋅⋅H contacts binding dimers (Figure 2a and Figure 4b) are represented by a close distance [2.328(2) Å], identified by the C···C distance of 4.240(2) Å. Several other H…H contacts can be identified in this region, however, they do not present directionality and short distances (see nest section). Due to geometry and supramolecular


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functionality, the nature and contribution of CH16H16⋅⋅⋅H16BC16 to crystal packing have been further investigated as followed .

Figure 2. (a) The crystal packing of AZN showing linear chains of dimers along the [010] plane mediated by C–H⋯O intermolecular hydrogen bonds, zigzag π···π interactions, and nonconventional homonuclear dihydrogen interaction (C−H···H−C) connecting a linear chain of dimers. Tetramer defined by A, B, C and D molecules. (b) C–H⋯O intermolecular hydrogen bonds evolving C1⋯O1, C7⋯O1 [symmetry code: x,y+1,z] and C16⋯O2 [symmetry code: x+1,-y+1,-z+1], donor/acceptor respectively along the [100] plane. (c) Representation of π···π interactions. Cg1 and Cg2 represent the centroids of aromatic rings [symmetry codes: i = -x,1-


12

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y,1-z; ii = 1-x,1-y,1-z]. To facilitate the comprehension, specific molecules in the crystal packing were ascribed by uppercase letters (A, B, C, D, E, F, G and F). HS analysis is an important tool for establishing the contribution of intermolecular interactions in the solid assembly of AZN. The HS and its corresponding 2D-plot of AZN are shown in Figure 3. On the dnorm surface (Figure 3a), red-light regions defined close to O-atoms are associated with H⋯O reciprocal contacts from C-H⋯O interactions. Similar regions are observed surrounding H-atoms from the C16 fragment and are attributed to close H⋯H contacts. Based on the shape of the index surface (Figure 3b), two complementary triangular patches are noted on the aromatic rings (Cg1) and (Cg2). This feature is attributed to the dimeric arrangement of π···π interactions.34 As showed previously, the packing of AZN presents a hydrophobic channel along the structure where C−H···H−C contact is established. In the 2D-plot (Figure 3c), the thin pike at di = de = 1.0 is indicative of the C−H···H−C contact, a dihydrogen interaction. Further, the small spikes located at di + de = 2.4 Å (Figure 3c) are characteristic of C−H···O interaction. Finally, the bright region around di = de = 2.0 Å is associated with C···C contacts characteristic of π···π stacking interaction, but they are not extensive, corresponding to 7.4% of HS. Considering the importance of the dihydrogen interactions, we provide a detailed view of its consistency in the next section, supported by combined QTAIM, NBO, global energy and CPMD approaches.


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Figure 3. (a) View of the Hirshfeld surface for AZN molecule mapped with dnorm property showing highlighted red points from H⋯O and H⋯H intermolecular contacts. Dashed lines represent the interactions. (b) Two views of the Hirshfeld surface mapped with shape index property showing complementary patches (red and blue), where π···π interactions occur. (c) The Fingerprint plot for AZN with highlighted traces related to O···H contacts (C−H···O interactions), C···C (π···π interactions) and H···H (C−H···H−C). Produced from de and di function mapped in color showing the percentage contribution of each type of interaction in total interactions verified. de - distance from the surface to the nearest atom exterior to the surface) against di - distance from the surface to the nearest atom interior to the surface).


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QTAIM, NBO and Global Energy Analysis. A crucial step in the study of weak interactions is the establishment that these interactions really exist. In this aspect, the most adequate method to ascribe the existence of an interaction is based on fulfilling the Popelier criteria30,35, defined from the QTAIM formulation32,33 The criteria are: i) existence of Critical Point (CP) between donor and acceptor atoms, ii) values of electron density [ρ(r)] in range of 0.002–0.035 a.u and, iii) Laplacian value of ρ(r) with range in 0.024 - 0.139 a.u at CP. Table 2. Topological and geometric parameters (in au and Ǻ) of the critical point discriminated in Fig.4 calculated at M062X/6-311G(d,p) level. Critical Point

R

ρ(rCP) (a.u.)

2

ρ(rCP) (a.u.)

ᐁ

Ε

G(rCP)

V(rCP)

E(rCP)

CP1

2.068

0.009

0.025

0.0098

0.0053

-0.0044

0.0009

CP2

2.475

0.004

0.013

0.1035

0.0028

-0.0022

0.0005

CP3

2.678

0.003

0.010

0.6821

0.0020

-0.0016

0.0005

CP4

2.554

0.004

0.014

1.4894

0.0028

-0.0022

0.0006

CP5

2.773

0.005

0.016

0.0793

0.0035

-0.0029

0.0006

CP6

2.520

0.008

0.026

0.0873

0.0058

-0.0051

0.0007

CP7

2.554

0.007

0.022

0.1060

0.0048

-0.0041

0.0008

Figure 4 presents the contour of the ρ(r) for AB-CD, BF and GH configurations of AZ molecules (Figure 2) at M06-2X level of theory. For the comparison of the strength and stability of these interactions, the topological properties of the CPs are listed in Table 2. Additionally, the topological analysis have also performed at wB97DX/6-311G(d,p) and APFD/6-311G(d,p) level, however, no significant changes have been found in the parameters (see Table S16 in ESI) when compared to those calculated by M06-2X one. The critical points CP1, CP2, CP3 and CP4 are


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involved in the dihydrogen interactions. It seems that CP1 exhibits higher accumulation of ρ than CP2, CP3 and CP4 ones, with ρ = 0.0090 a.u. and ∇2ρ(r) = 0.250 a.u (see Figure 4a). Consequently, only the critical point CP1 fulfils Popelier criteria30,35 to characterizes the topological parameters of a C−H···H−C interaction. This behavior stem from remarkable directionality and proximity between hydrogens27. For the GH configuration, the presence of the critical points (CP5, CP6 and CP7) is observed between O2G and three hydrogens in the H molecule (see Figure 4c), supporting the stability of the methyl group involved in the directional dihydrogen interaction. Indeed, the assumption of this work that the CH⋯HC interaction exists as a weak interaction in the AZN crystal structure, and its cooperative effect in the hydrophobic regions (Figure 2a) is confirmed on stabilization of supramolecular assembly of this crystal.


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Figure 4. Critical points for the (a) AB-CD configuration, (b) B-F and (c) G-H configurations of the AZN molecules calculated at M062X/6-311G(d,p) level. The same critical points were found at wB97XD and APFD level (see Table 2). Critical points are represented as yellow and orange circles. At critical points discussed in this work a specific nomenclature is ascribed. The consistency of C−H···H−C contact is further accessed by ellipticity parameter (ε) and the energies of electrons at CP [G(r), V(r) and E(r)]. Ellipticity is a parameter used to describe the character of the chemical interaction. Analyzing Table 2, it is observed that the


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ellipticity at CP1 ≅ 0 which indicate a "cylindrical" shape symbolizing a sigma bond-type. Elliptic value for CP2, CP3 and CP4 are higher, consequently, these interactions can be considered with pi bond-type20,83. These differences reinforce the relevance of CP1 in the stabilization of this crystalline structure. Furthermore, the combination of the signal and magnitude of

ᐁ

2

ρ, G(r), V(r) and E(r) parameters characterizes the degree of covalence and

strength of an interaction. For ᐁ 2ρ0 and E(r)0 and E(r)>0). These results support that AZN packing is assisted by longrange interactions, especially dihydrogen interactions, and their importance for the stabilization along the c axis. Since the existence of the C−H···H−C contact was identified by topological analyses, the nature and stability of this interaction can be accessed by localized natural bond orbitals analysis. It is evaluated from the interaction between filled orbitals of one subsystem and vacant orbitals of another one, also called hyperconjugation76–78,85. The hyperconjugation derived from NBO analysis for the arrangement of the two AZN dimers is presented in Table 3, and several observations are pointed out: (a) The Lewis donor BD(1)C16B-HαB bonding of molecule B is hyperconjugated with non-Lewis receptors RY*(1)HαC, RY*(2)HαC and BD*(1)C16C-HαC of molecule C. This results in a charge transfer of 0.0005e corresponding to 0.5 kcal.mol-1. (b) Similarly, the natural bond orbital on the Lewis donor C16C-HαC of molecule C hyperconjugates with the non-Lewis natural antibond orbitals BD*(1)C16B-HαB, the Rydberg orbitals RY*(2)HαB and RY*(1)HαB of molecule B. The hyperconjugation stabilization energy is also ca 0.5 kcal.mol-1, and the charge transfer is 0.0005e from molecule B to molecule C. This analysis


18

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shows that hyperconjugation accounts for 1.0 kcal.mol-1 of the energy interaction between molecules C and B. From NBO analyses, the nature of the stabilization of the C−H···H−C contact stems from the molecular orbitals and the charge transfer interaction between the C−H fragments, in agreement with the analysis in Ref. [21]. Table 3. Second order perturbation analysis of Fock matrix in NBO approach. E2

E(j)-E(i)

F(i,j)

(kcal.mol-1)

(a.u)

(a.u.)

0.08

1.83

0.011

BD (1) O2A -N3A

0.07

1.84

0.010

LP (2)O1A

0.18

0.93

0.012

0.05

0.87

0.007

0.12

0.94

0.010

Donor (i)

Acceptor (j)

From molecule A (D) to molecule B (C) BD(1)O1A - N3A

LP (3)O1A

RY*(1)HࢽB

BD*(1) C16B - HࢽB

LP (2)O2A

From molecule B to molecule C and vice versa RY* (1)HહC

0.25

1.61

0.018

RY* (2)HહC

0.15

2.63

0.018

BD* (1)C16C-HહC

0.10

1.28

0.010

BD(1)C16B-HહB

Another aspect of the C−H···H−C contact should be explained, taking into account the hindrance of the methyl rotation (molecule B), which it is feasible by the interaction with the nitro group (molecule A). This constraint can be related with the hyperconjugation between LP(2)O1A, LP(3)O1A and LP(2)O2A lone pair orbitals, with the antibonding BD*(1)C16B-HγB with an stabilization energy of 0.35 kcal.mol-1, which corresponds roughly to 3.5x10-5e. A minor hyperconjugation contribution is also observed from RY*(1)HγB orbital to BD(1)O1A-N3A and


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BD(1)O2A-N3A orbitals from molecule A, with a second order perturbation energy of 0.15 kcal.mol-1 (see Table 3). Similar behaviour is observed for the interaction between molecule C and molecule D (see Table 3). No hyperconjugation is observed between molecules B and D and between molecules A and C. The cooperative effect of CH⋅⋅⋅HC contacts on the stability of the AZN assembly can be extended by interaction energies calculated at APFD/6-311G(d,p) level: (i) the global energy interaction between A and B molecules (AB configuration) has a contribution around -20.67 kcal.mol-1 (Eq.1a), showing a strong stabilization of the dimeric arrangement. As ascribed by NBO analysis, the NO2A and C16B-HહB and π···π interactions play a major role in the stabilization of this dimer; (ii) the global interaction energy between B and F molecules (B-F configuration) with a contribution around -0.59 kcal.mol-1 (Eq.1b); (iii) the global interaction energy between G and H molecules (G-H configuration) with a contribution around -4.00 kcal.mol-1 (Eq.1c) and iv) the global interaction energy between AB and CD (AB-CD configuration) with a contribution around -0.58 kcal.mol-1 (Eq.2), reflects the accumulation effect of the C−H···H−C contacts and dispersion interactions throughout the hydrophobic regions. See Table S17 in ESI for comparison of interaction energy without and with BSSE correction in other levels of calculations. Molecular Dynamics simulation. In order to understand the dynamic nature of C−H···H−C contact for the crystal packing and also to support the C−H···H−C directionality, a CPMD of a system formed by the AZN dimers was carried out (see METHODS SECTION – Molecular Dynamics). This arrangement was used as a supramolecular assembly of solid-state of AZN, and the study was focused on the dynamics of C15B, C16B, C17B, O1A, O2A, N3A atoms and H-atoms that bonded them. From the CPMD simulations we conveniently monitored the


20

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following geometric parameters: HαB⋅⋅⋅HαC, HγB⋅⋅⋅O1A, HγB⋅⋅⋅O2A, HαB⋅⋅⋅HαC-C16C, HαB⋅⋅⋅HγBO1A, HαB⋅⋅⋅HγB-O2A and C16B-HαB⋅⋅⋅HαC-C16C (see Fig.5a). The HαB⋅⋅⋅HαC, C16B-HγB⋅⋅⋅O1A and C16B-HγB⋅⋅⋅O2A parameters have an average mean value of 2.208 Å, 133° and 138°, respectively. However, an abrupt deviation in these parameters can be observed at 19 ps, which is relative to a methyl group rotation torsion involved in the C−H···H−C contact. The average mean values of the HαB⋅⋅⋅HαC-C16C and C16B-HαB⋅⋅⋅HαC angles are around 151.4°±26° and 157.0°±13°, respectively, showing the linear directionality of the CH⋅⋅⋅HC interaction. Additional geometric parameters obtained from the CPMD approach can be found in the ESI file. The rotation around the C15−C16 bond results in an exchange between HαC and HβC positions; however, the initial CH⋅⋅⋅HC arrangement is re-established (see Figure 5b). The rotation of the methyl group (C16B) may compete with the stability of the CH⋅⋅⋅HC interaction, which is equivalent to around 1 kcal.mol-1 (see NBO analysis). The equivalent temperature to destabilize this interaction is around 500 K, a region in which the title azine does not exist as a crystal (see melting point in METHODS SECTION – Synthesis and crystallization). Furthermore, the torsion barrier energy of τ(C17C-C15C-C16C-HαC) is about 3.30 kcal.mol-1 (see Figure 5c). In a real system, this thermal energy is only accessed with an equivalent temperature above 1500 K. The conformational change of methyl groups was only observed in the simulation due to the constraint imposed on the system and the canonical thermostat, to ensure the description of the hydrophobic channel and temperature around 300 K, respectively.


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Figure 5. (a) Time evolution of HαB⋅⋅⋅HαC, HγB⋅⋅⋅O1A, HγB⋅⋅⋅O2A, HαB⋅⋅⋅HαC-C16C, C16BHαB⋅⋅⋅HαC, C16B- HγB⋅⋅⋅ O1A and C16B- HγB⋅⋅⋅ O2A geometrical parameters using CPMD method. (b) Time evolution of HαB⋅⋅⋅HβC, an HαB⋅⋅⋅HαC around the rotational event of the methyl group (C16) (c) Potential energy curve of the C17C-C15C-C16C-HαC torsional angle from 0° to 360° at the M062X/6-311G(d,p) level.


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CONCLUSIONS The quantum chemical and structural investigation reported here was devoted mostly to the homonuclear dihydrogen interaction aspects in the crystalline environment. In general, the C−H···H−C contact is neglected in the supramolecular analyses in solid-state, in view of a myriad of classical intermolecular interactions. However, in the AZN, the weak interactions have presented a relevant contribution to the stability of molecular packing, in which the C−H···H−C contact plays a fundamental role. Remarkably, C−H···H−C contacts as individual entities are negligible; however, by their cooperative effect on AZN packing, they make a significant contribution in the supramolecular stabilization, according to the Gulliver principle.3,24,86 The following key findings emerged from our investigation and support the existence of C−H···H−C contacts:

•

The packing of AZN forms a hydrophobic channel along the structure, where these contacts are established.

•

The directional C−H···H−C contact presents at a critical point (CP1), ρ = 0.0090 a.u. and ∇2ρ(r) = 0.250 a.u. observed between H atoms. These topological parameters fulfil the criteria to characterize a dihydrogen interaction.

•

The

ᐁ

2

ρ and E(r) parameters on the CP1 are positive, ascribing a dihydrogen

interaction with a weak character.

•

Additional critical points (CP2, CP3 and CP4) are involved with dihydrogen contacts, however, they do not fulfil the Popelier criteria.


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•

Page 24 of 39

The BD(1)C16B-HαB, RY*(1)HαC RY*(2)HαC, BD*(1)C16C-HαC orbitals are involved in the hyperconjugative nature of the C−H···H−C contact. This analysis shows that the hyperconjugation accounts for 1.0 kcal.mol-1 of the energy for this interaction.

•

From NBO analyses, the nature of the stabilization of the C−H···H−C contact stems from the molecular orbitals and the charge transfer interaction between the C−H fragments, in agreement with the analysis in Ref. [21].

•

The global energy analyses suggest that the O2A⋯HγB and π···π interactions are responsible for the dimer formation with an interaction energy around 21 kcal.mol-1.

•

The constraint on specific atoms of the tetramer and considering a canonical thermostat conditions the torsion around the methyl group (C16B). However, the initial C−H···H−C arrangement is re-established. In a real system, this torsion barrier energy is just accessed with a thermal energy above 1500 K, a region in which the title azine does not exist as a crystal.

We expect that the comprehension and description of homonuclear dihydrogen interactions in the supramolecular assembly of the C17H17N3O2 can assist in the crystal engineering of azine and analog molecules, offering progress in the physical-chemistry parameters of biological and material processes. ASSOCIATED CONTENT Supporting Information. The Supporting Information is available: 1H NMR,

13

C NMR, Infra-

red (IR) spectra, Gas chromatography–mass spectrometry (GC-MS), X-ray structural analysis,


24

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2D fingerprint plots of remaining contacts from HS, , topological analysis, selected bond length, angles and dihedral angles from molecular dynamics and selected hydrogen bonds geometry. Accession Codes. CCDC 1489316 contain the supplementary crystallographic data for this AZN structure. These data can be obtained free of charge via www.ccdc.cam.ac.uk/data_request/cif, or by emailing [email protected], or by contacting The Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, UK; fax: +44 1223 336033. AUTHOR INFORMATION Corresponding Author * E-mail: [email protected] (P. S. Carvalho Jr). * E-mail: [email protected] (V. H. Carvalho-Silva). Present Addresses †If an author’s address is different than the one given in the affiliation line, this information may be included here. Author Contributions The manuscript was written through contributions of all authors. All authors have given approval to the final version of the manuscript. All these authors contributed equally. Notes The authors declare no competing financial interest.


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ACKNOWLEDGMENT The authors acknowledge the Brazilian funding agencies Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) – P.S.C.-Jr. grant 12/05616-7, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) and Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) for financial support. V. H. C. Silva thanks PrP/UEG for research funding through the PROBIP and PRÓ-PROJETO programs. Also, the authors would like to thank the University of Durham for access to their X-ray facilities. ABBREVIATIONS DHB, Dihydrogen bond; TLC, Thin layer chromatography; DFT, Density functional theory; HS, Hirshfeld surface; QTAIM, Quantum theory of atoms in molecules; NBO, Natural bond orbitals; CPMD, Car-Parrinello molecular dynamics.

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For Table of Contents Use Only Title: The Contribution of Directional Dihydrogen Interactions in the Supramolecular Assembly of Single Crystals: Quantum Chemical and Structural investigation of C17H17N3O2 Azine Authors: Leonardo R. de Almeida,§ Paulo S. Carvalho-Jr,*§ Hamilton B. Napolitano,§ Solemar S. Oliveira,§ Ademir J. Camargo,§ Andreza S. Figueredo,§ Gilberto L. B. de Aquino,§ and Valter H. C. Silva.*§

Synopsis: The supramolecular assembly of the C17H17N3O2 Azine derivative is established by intermolecular interactions CH···O, π···π and, remarkably, the hydrophobic directional C−H···H−C contact. All of those were observed in the crystal structure and, together, played an important role. This work has focused on the relevance of C−H···H−C contact in crystal packing, summarized by Hirshfeld surface, QTAIM, NBO and CPMD approaches.


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Fig 1.



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Fig 2. 990x776mm (96 x 96 DPI)


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Fig 3. 798x725mm (150 x 150 DPI)



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Fig 4. 1422x1422mm (96 x 96 DPI)


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Fig 5. 506x863mm (200 x 200 DPI)


Contribution of Directional Dihydrogen Interactions in the

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