Experimental X-ray Diffraction Study of Stacking Interaction in Crystals

Article pubs.acs.org/crystal

Experimental X‑ray Diffraction Study of Stacking Interaction in Crystals of Two Furazan[3,4‑b]pyrazines Published as part of the Crystal Growth & Design Mikhail Antipin Memorial virtual special issue Boris B. Averkiev,*,†,‡ Alexander A. Korlyukov,‡,§ Mikhail Yu. Antipin,†,‡ Aleksei B. Sheremetev,∥ and Tatiana V. Timofeeva† †

Department of Biology and Chemistry, Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Las Vegas, New Mexico 87701, United States ‡ Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Vavilov str. 28, Moscow, 119991, Russia § Pirogov Russian National Research Medical University, Ostrovitianov str. 1, Moscow, 117997, Russia ∥ Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prosp. 47, Moscow, 119991, Russia ABSTRACT: The molecular and crystal structures of two energetic fused furazans, 4H,8H-bis-furazano[3,4-b:3′,4′-e]pyrazine (1) and 4H,9H-bisfurazano[3,4-b:3′,4-g]-pyrazino[2,3-e]pyrazine (2), have been studied by single crystal X-ray diffraction analysis. These materials were found to have rather high crystal densities for organic compounds (2.032 and 1.882 g·cm−3). Very short interplanar distances between overlapping molecules in crystals (less than 3.15 Å) suggest the presence of stacking interaction between planar rings. High-resolution lowtemperature X-ray diffraction data for both compounds were used to analyze the electron density distribution in the area of stacking interaction and hydrogen bonds, as interpreted through the framework of Bader’s AIM theory. A weak accumulation of the electron density, and (3, −1) bond critical points were found in the area of this interaction between overlapping molecules in the crystal. It was established that the energy of the stacking interactions in 1 and 2 are 3.9 and 3.2 kcal/mol, which is in good agreement with previous experimental and theoretical works. On the basis of our results and literature data we analyzed the correlation between the interatomic distance and the electron density in critical point (3, −1). This analysis revealed that the stacking interaction is a partial case of other specific interactions.

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INTRODUCTION Intermolecular interactions like hydrogen bonds, stacking interactions, specific nonbonding interactions, and so forth form the basis of modern supramolecular chemistry. These interactions govern the structure and properties of molecular crystals,1−5 DNA,6,7 and different molecular associates in solutions.8 The two most common specific intermolecular interactions are hydrogen bonding and stacking, the interaction between overlapping planar and parallel π-systems of aromatic fragments. The role of hydrogen bonding in crystal structure formation has been investigated intensively over the past few decades,1 and the importance of accounting for these types of interactions in understanding many features of crystal structures is well-established.9−11 Conversely, the nature of the weaker interaction, intermolecular stacking, has received less attention in the literature. Two main approaches were used to describe the nature of stacking interaction. The first one relates stacking to a charge transfer between π-systems of overlapping molecules,12−14 while the second considers stacking as an electrostatic interaction.15−17 Both these models are based on energy calculations,18,19 optical spectra,12,13 and analysis of crystal packing (in particular, distances between overlapping planar © 2014 American Chemical Society

molecules or their fragments), including statistical analysis of corresponding data from the Cambridge Structural Database (CSD).4,20 It seems reasonable, however, that the most important approach to making more definitive conclusions about the nature of stacking interactions is the study of the electron density distribution (EDD) and its characteristics in the area between overlapping molecules. The EDD may be calculated using quantum chemistry methods or obtained experimentally from the high-resolution X-ray diffraction data.21 Over the past several decades, theoretical methods and X-ray diffraction techniques have achieved a level that has greatly facilitated the study of EDD in crystals. However, even now most results for stacking interactions are obtained from theoretical calculations, while there are still not many experimental investigations of the EDD for structures with stacking interactions. In this paper we report application of the analysis of experimental electron density distribution and its topology for detailed description of the molecular structure and stacking Received: April 25, 2014 Revised: September 21, 2014 Published: September 23, 2014 5418

dx.doi.org/10.1021/cg500589f | Cryst. Growth Des. 2014, 14, 5418−5427

Crystal Growth & Design

Article

function. In the AIM theory, critical points (CP’s) are those where the electron density gradient vanishes, and the presence of the most important critical point (3, −1) between two atoms (saddle point in the ρ(r) relief) is the universal indicator of chemical bonding. In addition to analysis of the chemical bonding pattern and direct estimation of molecular and crystal properties (including crystal packing energy25,27−29), this analysis makes it possible to answer the question “do the shortened intra- and/or intermolecular nonbonded distances in a crystal correspond to attractive interactions?″. The energy of interatomic (noncovalent) interactions may be estimated using Espinosa’s equation based on the potential energy density, Vb, in a bond critical point (3, −1) of this contact30

interactions in crystals of fused furazans, 4H,8H-bis-furazano[3,4-b:3′,4′-e]pyrazine (1) and 4H,9H-bis-furazano[3,4-b:3′,4g]pyrazino[2,3-e]pyrazine (2).

Compound 1 has one six-membered ring and two fivemembered rings in its molecule. Compound 2, that combines the same rings, has an additional six-membered ring. These compounds were chosen because of the very short (less than 3.15 Å) distances between planes of fused cyclic systems of adjacent molecules in their crystals. This geometrical feature may suggest importance of stacking interactions in crystals of 1 and 2. The presence of specific intermolecular interactions is manifested in the high crystal density of compounds (2.032 and 1.882 g·cm−3, respectively); therefore, 1 and 2 and their derivatives may be considered as prospective high-energetic materials. To reconstruct experimental EDD in an analytical form, the multipole refinement of diffraction data using the HansenCoppens formalism22 and XD program package23 is usually applied. In the framework of the multipole model 22 experimental electron density in a crystal is described in analytical form as a sum of rigid pseudoatom densities at the nuclear positions (Rj)

E int = −0.5Vb

(3)

The potential energy density V(r) is related to the kinetic energy density G(r), and the electron density Laplacian ∇2ρ(r) via the local virial theorem25 2G(r) + V (r) = 1/4∇2 ρ(r)

(4)

In turn, the G(r) value may be obtained from the ρ(r) using the Kirzhnitz approximation for the kinetic energy density.31,32 According to this approximation, the value of the G(r) is equal to G(r) = (3/10)(3π 2)2/3 [ρ(r)]5/3 + (1/72)|∇ρ(r)|2 /ρ(r) + 1/6∇2 ρ(r)

(5)

(2)

This approach allows estimation of both kinetic and potential energy density. It should be noted also that usage of the above approximation for the kinetic energy density allows calculation of the electron localization function (ELF) directly from the experimental diffraction data.33 Such topological analysis of the experimental EDD has been previously applied to study stacking interaction in crystals of pcyclophane,34 in 3,4-diamino-1,2,4-triazole,35 and in crystalline α-form of picolinic acid N-oxide.36

where both the ρcore and ρval describe the frozen core with fixed population Pcore and spherical valence population Pval, respectively. Both the ρcore and ρval varied to allow charge transfer between atoms. The κ variable allows for contraction or expansion of the electron charge cloud of the pseudoatom. The last term in the equation describes nonsphericity of the valence density via a set of deformation functions (multipoles) composed of spherical harmonics (dlm) and radial Slater-type functions with expansion−contraction coefficient κ′. All these parameters are refined by least-squares together with other crystallographic parameters (atomic coordinates, anisotropic displacement parameters, etc.) against experimental structure factors. The correctness of the multipole refinement is supported not only by the R-values, but also via analysis of the anisotropic displacement parameters (Hirshfeld’s “rigid-bond” test24) and residual electron density maps. Topological analysis of the experimental electron density distribution ρ(r), based on X-ray diffraction data analyzed with the multipole model and using Bader’s “Atoms in Molecules” (AIM) theory,25 gives an additional extraordinary opportunity to examine valuable characteristics of chemical bonding in molecules and crystals.26 In particular, this analysis provides a tool to determine attractive interatomic interactions in crystals by a search for critical points of the three-dimensional ρ(r)

Compound 137,38 (mp 294−295 °C) and 239 (mp 317−321 °C) were synthesized using the published procedure. Suitable for X-ray analysis, single crystals of both compounds were grown by slow cooling of a water solution. High-resolution low-temperature X-ray diffraction experiments for compounds 1 and 2 (at 110 and 150 K) were performed with the Bruker SMART CCD and SyntexP21 diffractometers, respectively. Data reduction was carried out with the SAINT40 and SADABS41 programs for 1 and SHELXTL PLUS42 program package for 2. The structures were solved by direct methods and refined by the full-matrix least-squares technique against F2 in the anisotropic approximation for non-hydrogen atoms. Hydrogen atoms were located from the difference Fourier synthesis and refined in the isotropic approximation. Important data collection parameters, crystal data, and results of the conventional refinement are summarized in Table 1. The multipole refinement was extended to the octupole level (l = 3) for all non-hydrogen atoms and to the quadrupole (l = 2) level for hydrogens. The positions of non-hydrogen atoms were refined using high-order reflections with |F| > 6.0σ(F) and sin θ/λ > 0.70 Å−1. The scattering factors for hydrogen atoms were calculated from the contracted radial density function with fixed expansion−contraction factor (κ = 1.2). Because hydrogen atoms in both molecules participate in strong hydrogen bonds, we did not use the standard values obtained from neutron diffraction data for the N−H bond lengths. Instead, we used distances obtained from quantum-chemical calculations of the

ρ (r ) =

∑ ρj (r − R j) (1)

j

Each pseudoatom electron density has the form ρatom (r ) = Pcoreρcore (r ) + Pvalκ 3ρval (κr ) l max

+

l

∑ κ′3Rl(κ′r) ∑ l=0

m =−1

Plmdlm(θ , ϕ)

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EXPERIMENTAL SECTION



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Table 1. Crystal Data and Structure Refinement Results for Compounds 1 and 2 1 empirical formula formula weight, g mol−1 crystal system space group Z temp, K wavelength, Å a, Å b, Å c, Å β, deg V, Å3 ρcalc, g cm−3 F(000) μ, mm−1 scan method 2θmax, deg no. of collected reflns no. of independent reflns no. of independent reflns with I > 2σ(I) Rint R(F) for reflns with I > 2σ(I) Rw(F2) for all independent refln goodness-of-fit no. of variables

2

C4H2N6O2 116.12 monoclinic P21/n 2 110 0.71073 (Mo Kα) 5.1253(1) 4.4839(1) 11.8178(3) 91.072(1) 271.54(1) 2.032 168 0.17 φ and ω 80 6876 1645 1494

C6H2N8O2 218.16 monoclinic P21/n 2 150 0.71073 (Mo Kα) 5.787(1) 11.646(2) 5.806(1) 100.21(2) 385.2(1) 1.881 220 0.15 θ/2θ 100 10650 4011 2605

0.0193 0.0424 0.0885 1.109 59

0.0348 0.0362 0.0948 0.916 77

Figure 1. General view of molecules 1 and 2 with atom numbering scheme. Displacement ellipsoids are drawn at the 50% probability level. Suffix A represents symmetry code (1 − x, 1 − y, 1 − z).

substituents result in lengthening of the N−O furazan bond.47−52 In both crystals molecules are arranged into the H-bonded ribbons formed by the translationally identical molecules (Figures 2a and 3a). However, due to different mutual orientation of ribbons, the motifs of crystal packing in these crystals are different. In the structure of tricyclic compound 1 the packing motif is more complicated. The ribbons are extended in two directions: [110] and [11̅0] (Figure 2b). In the tetracyclic structure 2 all ribbons are extended in the [100] direction and arranged in a herringbone motif (Figure 3b). In this crystal the ribbons are almost perpendicular: the angle between them is equal to 87°. Unlike structure 2, in structure 1 there are additional intermolecular hydrogen bonds between nonparallel neighboring ribbons: the hydrogen atom H(1) participates in the bifurcate hydrogen bond with the N(1) atom of furazan subunit of the molecule from the same ribbon, and with the N(2) atom of furazan subunit of molecule from perpendicular ribbon (Figure 2a). As a result, hydrogen bonds in structure 1 create the three-dimensional network, while in structure 2 a one-dimensional system of hydrogen bonds is observed. In structure 1 both nitrogen atoms of the furazan subunit participate in the intermolecular hydrogen bonding (Figure 2a), while in structure 2 the intermolecular hydrogen bonding is organized by nitrogen atoms of the pyrazine subunit (Figure 3a). The geometrical parameters of the hydrogen bonds are summarized in Table 3. It is noteworthy that in structure 1 there are other shortened intermolecular contacts, connecting perpendicular ribbons: O(1)···O(1) 2.850 Å and O(1)···N(2) 2.914 Å (the corresponding sums of van der Waals radii53 are 3.12 and 3.17 Å). The most interesting feature of the both crystal structures is a partial overlap of molecules belonging to parallel ribbons

hydrogen-bonded trimer (for structure 1) and the dimer (for molecule 2), in accord with features of their crystal packing (see below). In these calculations the positions of non-hydrogen atoms (taken from X-ray experiment) were fixed and only hydrogen positions were refined. The obtained values of the N−H bonds were found to be 1.03 and 1.04 Å for molecules 1 and 2, respectively. All bonded pairs of atoms satisfy the Hirschfeld’s “rigid-bond” criteria24 (differences of the mean square displacement amplitudes along the bonds were not larger than 8 × 10−4 Å2). The residual electron density did not exceed 0.12 eÅ−3. The experimental electron density distribution in structures 1 and 2 was analyzed further in the framework of Bader’s theory of “Atoms in Molecules” (AIM).25 Results of the analysis of the EDD for 1 and 2 were obtained from XDPROP module in the XD package program.23 Quantum-chemical calculations were performed using the Gaussian03 program43 at the B3LYP/6-311G** level. Analysis of the topology of the experimental ρ(r) function was carried out using the WINXPRO program package.44

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RESULTS AND DISCUSSION Molecular and Crystal Structure. The general view of molecules 1 and 2 is presented in Figure 1. Both molecules occupy the crystallographic inversion centers. The approximate local symmetry of the tricyclic molecule 1 is D2h, while the tetracyclic molecule 2 possesses C2h symmetry. Their geometric parameters are given in Table 2. The C−C and C−N bond lengths of the furazan fragment are close to the average values from the CSD45,46 (1.428 and 1.299 Å for C−C and C−N bonds, respectively), while N−O bonds in molecule 1 and N(2)−O(1) bond in molecule 2 are slightly longer than the mean N−O value 1.385 Å from the CSD. The latter small lengthening may be related to the donor nature of the neighboring N−H group; it was noted earlier that donor 5420



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Table 2. Geometrical Parameters of Molecules 1 and 2a 1 O1−N1 O1−N2 N1−C1 N2−C2 N3−C1 N4−C2b C1−C2 C3−C3A N3−C3A N4−C3 N1−O1−N2 C1−N1−O1 C2−N2−O1 C3A−N3−C1c C3−N4−C2c C3−N4−H1d C2−N4−H1e N1−C1−N3 N1−C1−C2 N3−C1−C2 N2−C2−N4b N2−C2−C1 N4−C2−C1b N3A−C3−N4 N3A−C3−C3A N4−C3−C3A

Bond, Å 1.4029(6) 1.3955(7) 1.3040(7) 1.3014(7) 1.3730(6) 1.3763(7) 1.4425(7)

Angle, deg 111.20(4) 104.68(4) 105.27(4) 114.89(4) 114.89(4) 118.7(10) 124.5(10) 128.01(5) 109.64(4) 122.34(5) 127.99(5) 109.21(5) 122.76(4)

N(1)−O(1) bond participates in the overlay, while the bond N(2)−O(1) does not. The distance between mean planes of overlapping molecules is 3.086 and 3.118 Å for structures 1 and 2, respectively. Such short interplanar distances are significantly less than the standard value of 3.5 Å and suggest the presence of stacking interactions between π-systems of overlapping molecules. The shortened intermolecular contacts in the area of overlap are C(1)···C(1′) 3.161(1), O(1)···N(3′) 3.093(1), and C(1)···N(1′) 3.191(1) Å for structure 1, and C(1)···C(1′) 3.182(1), O(1)···N(3′) 3.219(1), and O(1)···C(3′) 3.154(1) Å for structure 2 (the corresponding sums of the van der Waals radii:53 C···C 3.5, O···N 3.17, C···N 3.36, C···O 3.31 Å). Due to very short intermolecular distances between planar molecules both of them have high densities for organic C, N, O, H-containing compounds: 2.032 and 1.882 g·cm−3, for 1 and 2, respectively. It is noticeable that according to the CSD data, compound 1 is one of the densest structures found among all organic compounds containing only C, H, N, and O atoms. Charge Density Distribution. A conventional method for the visualization of the charge density redistribution due to the formation of chemical bonds in a molecule is the deformation electron density (DED) mapping.21,26 The static multipole DED maps for molecules 1 and 2 are presented in Figure 5. Both maps clearly demonstrate accumulation of the electron density on covalent bonds as well as in the areas of the lone pairs of nitrogen and oxygen atoms. For N−O bonds in both structures the positive DED is very small or even close to zero (in structure 1). This DED feature is well-known for single bonds between electronegative atoms21 having more than halffilled valence shells and it is related to a cumulative diminution of the electron density in the construction of the DED maps. The DED sections in the planes perpendicular to the molecular planes and passing through the terminal oxygen atoms are presented in Figure 5c,d. It is seen from these sections that oxygen atoms have two nonseparated DED maxima (0.6−0.8 e Å−3) corresponding to the lone electron pairs. Formally single C−C bonds have a noticeable πcomponent suggesting some electron density delocalization in

2 1.3890(6) 1.4011(6) 1.3092(6) 1.3049(6) 1.3688(6) 1.3671(6) 1.4196(6) 1.5054(7) 1.3192(5) 1.3483(5) 112.21(3) 104.15(4) 103.53(4) 115.66(3) 118.21(3) 119.7(7) 122.0(7) 126.81(4) 109.65(4) 123.53(4) 128.77(4) 110.45(4) 120.75(4) 118.18(3) 122.93(4) 118.89(4)

Suffix A represents symmetry code (1 − x, 1 − y, 1 − z). bFor molecule 1 N3A should be instead of N4. cC1−N3−C2A for molecule 1. dC2A−N3−H1 for molecule 1. eC1−N3−H1 for molecule 1. a

(Figure 4). The schemes of molecular superposition are similar in both cases: terminal furazan fragment overlays with the central fragment of a neighboring molecule. In both cases the

Figure 2. Scheme of hydrogen bonding in the structure 1 (a) and projection of the crystal packing along the [110] direction (b). 5421



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Figure 3. Scheme of hydrogen bonding in the structure 2 (a) and projection of the crystal packing along the [100] direction (b).

Table 3. Geometrical Parameters of H-Bonds in Structures 1 and 2 structure

D−H···A

D···A, Å

D−H, Å

H···A, Å

DHA, deg

1 1 2

N3−H1···N1 (2 − x, 2 − y, 1 − z) N3−H1···N2 (x + 0.5, 1.5 − y, z + 0.5) N4−H1···N3 (x − 1, y, z)

3.2995(7) 2.9909(6) 2.9237(7)

0.91(1) 0.91(1) 0.88(1)

2.61(1) 2.214(15) 2.06(1)

133(1) 143(1) 165(1)

In Table 4 the topological characteristics of chemical bonds in 1 and 2 in the (3, −1) bond critical points are presented including the electron density ρ(r), its Laplacian ∇2ρ(r), and bond ellipticityies (ε), showing the contribution of the πcomponent into the bonding.25 According to these data, single N−O bonds have the smallest values of the electron density in the (3, −1) bond critical points, small ellipticities (almost no πcomponent), and are characterized by positive values of the electron density Laplacian. This is a typical feature of the single polar bonds. On the other hand, all other bonds are characterized by negative values of the Laplacian and values of bond ellipticity demonstrating electron density delocalization in the central part of the molecules studied. The negative Laplacian maps in molecular planes of 1 and 2 are presented in Figure 6, also showing a specific nature of the N−O bonds. To estimate atomic charges in molecules 1 and 2, we used Bader’s approach25 in the topological analysis of the EDD and have determined the atomic basins (Ω) and their volumes surrounded by the electron density gradient zero-flux surface and have integrated the ρ(r) over each Ω (Table 5). The sum of obtained atomic volumes reproduces the unit cell volume per molecule in compounds 1 and 2 with very high accuracy (the difference 0.12−0.14%). The charges in furazan subunits calculated by integration of the Ω are close in both molecules. As expected, in the furazan rings the oxygen and nitrogen atoms are negatively charged and positive charge is localized on the C(1) and C(2) atoms. Analysis of Stacking Interactions. One of the most interesting and valuable applications of topological analysis of

Figure 4. Scheme of molecular overlap in crystal structures 1 and 2. Primed atoms are related to the basis ones by symmetry operation 1 − x, 1 − y, 1 − z.

the molecules. These conclusions are in line with analysis of the EDD topology in the crystals of 1 and 2 (Table 4). 5422



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Figure 5. Static deformation electron density (DED) maps in the mean planes of molecules 1 (a) and 2 (b) and in planes perpendicular to the molecular planes of 1 (c) and 2 (d) and passing through the terminal oxygen atoms. The contour intervals are 0.1 e Å−3. Solid lines and dashed lines represent positive and negative DED values, respectively.

Table 4. Topological Characteristics of the Electron Density at the (3, −1) Bond Critical Points in Structures 1 and 2a 1 bond O1−N1 O1−N2 C1−N1 C2−N2 C1−C2 C1−N3 C2−N4b C3−N4 C3A−N3 C3−C3A N4−H1c a

−3

−5

2 −3

ρ, e Å

∇ ρ, e Å

ε

d, Å

1.984 1.972 2.604 2.719 2.033 2.275 2.178

9.668 9.061 −25.414 −29.330 −17.346 −21.424 −16.327

0.08 0.07 0.29 0.22 0.25 0.21 0.25

1.4001 1.3929 1.3042 1.3013 1.4449 1.3726 1.3766

2.237

−32.495

0.07

1.02

2

−5

ρ, e Å

∇ ρ, e Å

2.161 2.084 2.562 2.651 2.181 2.241 2.204 2.336 2.481 1.868 2.362

6.527 7.498 −27.488 −27.277 −19.697 −19.823 −19.072 −23.934 −24.235 −14.249 −49.433

2

ε

d, Å

0.09 0.03 0.14 0.18 0.19 0.19 0.17 0.18 0.22 0.20 0.04

1.3839 1.3999 1.3072 1.3048 1.4220 1.3661 1.3663 1.3489 1.3183 1.5052 1.04

Suffix A represents symmetry code (1 − x, 1 − y, 1 − z). bC2−N3A for molecule 1. cN3−H1 for molecule 1.

from the other intermolecular interactions. The value of electron density on its critical point is 0.226 e Å−3, that is 3− 5 times larger than the values for the other critical points, ranging from 0.02 to 0.08 e Å−3. The obtained energy (using eq 3) for the N4−H1···N3 hydrogen bond is 6.92 kcal/mol. This value is close to the energy of the N−H···O hydrogen bond (6.21 kcal/mol) in 2-trifluoroacetyl-5-trifluoromethylpyrrole.54 Hydrogen bonds H1···N2 and H1···N1 in tricyclic structure 1 are considerably weaker (2.97 and 1.05 kcal/mol, respectively). However, the sum of energies of these interactions (the total energy of the bifurcate hydrogen bond) is 4.02 kcal/mol, which is comparable to the energy of the hydrogen bond in tetracyclic structure 2. The parameters of electron density in the critical points corresponding to stacking interaction are given in Table 6. According to the energy calculated from eq 3, in both structures

the EDD is investigation of the electron density and its characteristics (including the energy of intermolecular interactions) in the area of nonbonded atomic contacts in the molecular crystals. As mentioned above, in both structures three types of short intermolecular contacts can be considered: (1) hydrogen bonds N−H···H, (2) stacking interactions in the areas of molecular overlap, and (3) intermolecular interactions between oxygen and nitrogen atoms. The topological analysis reveals the presence of critical points in all three cases. These points are presented in Figures 7 and 8. Unlike the hydrogen bonds and O···O interactions, the stacking interactions are represented by the three critical points, located between C1···C1, O1···N3, and symmetrically equivalent N3··· O1 atoms. The values of electron density, ρ(r), and Laplacian, ∇2ρ(r), in these critical points are given in Table 6. The strong hydrogen bond N4−H1···N3 in structure 2 is notably different 5423



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Figure 6. Laplacian of the electron density through the mean planes of molecules 1 and 2. Solid and dashed lines represent negative and positive Laplacian values, respectively.

the C1···C1 interactions are slightly stronger than the O1···N3 interactions. The total energy of stacking interaction (2 × O1··· N3 + C1···C1) is equal to 3.9 and 3.2 kcal/mol for structures 1 and 2, respectively. Hence, there is a correlation between the energy of the stacking interaction and the interplanar distance in structures 1 and 2 (3.086 and 3.118 Å). The obtained energies are in good agreement with previously reported values of 3.6 and 3.8 kcal/mol for the stacking interaction in 3,4diamino-1,2,4-triazole,35 and in picolinic acid N-oxide,36 respectively. The electron density distribution in the area of the stacking interaction is presented in Figure 9. It can be seen that an electron density distribution between overlapping molecules corresponds to the character of overlapping: there is an accumulation of electron density in the areas of shortest intermolecular contacts, C1···C1 and N3···O1 (see also Figure 4). The energy of other intermolecular interactions ranges from 0.41 (N1···N2 in 2) to 1.92 kcal/mol (O1···O1 in 1). This is in an agreement with the value of 1.31 kcal/mol obtained for O···

Table 5. Calculated Atomic Charges and Volumes in Structures 1 and 2 V, Å3

Z, e atom

1

2

O(1) N(1) N(2) N(3) N(4) C(1) C(2) C(3) H(1) Vmola Vmol expb

−0.30 −0.33 −0.33 −0.91

−0.24 −0.31 −0.31 −1.08 −0.76 0.64 0.72 0.72 0.37

0.69 0.65 0.53

1 11.56 13.93 12.97 12.76 7.02 7.15 2.39 135.61 135.77(1)

2 12.60 16.75 14.98 14.07 14.65 7.61 6.55 7.59 1.35 192.3 192.6(1)

a

The molecular volume has been calculated by summation of atomic volumes. bThe experimental molecular volume has been calculated by dividing of the volume of unit cell by Z.

Figure 7. Bond critical points in structure 1 corresponding to the intermolecular contacts in the area of stacking interaction (a), and corresponding to the hydrogen bonds and O···O contact (b). The parameters of critical points are presented in Table 6. 5424



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Figure 8. Bond critical points in structure 2 corresponding to the area of intermolecular stacking interaction (a), and to the hydrogen bond (b). The parameters of critical points are presented in Table 6.

Table 6. Topological Characteristics of the Electron Density at the (3, −1) Bond Critical Points of Nonbonded Contacts in Structures 1 and 2 contact N1···H1 N2···H1 C1···C1 O1···N3 O1···O1 N1···N1 N2···N2 N3···N3 N3···H1 C1···C1 O1···N3 O1···N1 N1···N2 N1···N4

symmetry codea

ρ, e Å−3

Structure 1 2 − x, 2 − y, 1 − z 0.034 x − 0.5, 1.5 − y, z 0.081 − 0.5 1 − x, 2 − y, 1 − z 0.060 2 − x, 2 − y, 1 − z 0.047 1.5 − x, 0.5 + y, 0.5 0.062 −z 2 − x, 2 − y, 1 − z 0.029 0.5 − x, 0.5 + y, 0.5 0.040 −z 2 − x, 1 − y, 1 − z 0.028 Structure 2 x + 1, y, z 0.226 1 − x, 1 − y, −z 0.052 1 − x, 1 − y, −z 0.042 x − 0.5, 0.5 − y, z 0.054 − 0.5 x + 1, y, z 0.018 x + 0.5, 0.5 − y, z − 0.025 0.5

∇2ρ, e Å−5

d, Å

−E, kcal/mol

0.721 1.689

2.5030 2.1622

1.05 2.97

0.660 0.746 1.099

3.1593 3.0991 2.8893

1.40 1.27 1.92

0.462 0.634

3.2275 3.101

0.71 1.04

0.409

3.4176

0.64

0.604 0.592 0.594 0.813

1.9176 3.1818 3.2482 3.0522

6.92 1.18 1.02 1.46

0.296 0.374

3.4942 3.4367

0.41 0.57

Figure 9. Electron density distribution between overlapping molecules in structures 1 and 2 reveals that the character of distribution corresponds to character of overlapping. The contour intervals are 0.01 e Å−3. The maxima of distribution correspond to the shortest intermolecular contacts.

a

The symmetry code applies to the second atom named for the contact.

F contact.54 The total energy of intermolecular interactions equals to 19.22 kcal/mol in 1 and 21.96 kcal/mol in 2. There are many publications devoted to the investigation of hydrogen bonding, so it was interesting to compare our results with the published data. It is quite obvious that for hydrogen bonds with shorter distances (bond path length) between the hydrogen and acceptor atoms the value of the electron density at the bond critical points is higher than for corresponding bonds with longer distances. Such a correlation was shown in several experimental and theoretical investigations of electron density distribution for hydrogen bonds. It was described for N−H···O and N−H···N bonds in dimers and trimers of DNA bases (adenine, guanine, cytosine, and thymine),55 obtained

using DFT calculations. In the experimental (X-ray diffraction) investigations of ionic complexes of 1,8-bis(dimethylamino)naphthalene with four different acids56 such a correlation was shown for the covalent bonds with the hydrogen atoms and for different types of weak interactions, including hydrogen bonds. In both cases dependence between the length of hydrogen bond and the value of electron density at the bond critical point is described as exponential. In Figure 10, we present an analogous graph using an extended set of literature data and data from our investigation. This graph comprises different types of hydrogen bonds: in 5425



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energy of hydrogen bond and is in good agreement with previous experimental investigations of stacking interaction.

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AUTHOR INFORMATION

Corresponding Author

*E-mail: [email protected]. Present Address

Boris Averkiev, The Richard Stockton College of New Jersey, School of Natural Sciences and Mathematics, Galloway, New Jersey 08205, USA. Notes

The authors declare no competing financial interest.

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ACKNOWLEDGMENTS The authors are grateful to NSF for DMR-0934212 PREM grant and Russian Science Foundation 14-13-00884 grant. A.B.S. thanks the Russian Science Foundation (grant number 14-13-01153).

Figure 10. Exponential dependence (solid line) between length of hydrogen bond H···Y (Y = N, O) and electron density in the corresponding critical points. The parameters of both intermolecular and intramolecular hydrogen bonds were used, as well as the parameters of covalent N−H and O−H bonds.

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REFERENCES

(1) Desiraju, G. R.; Steiner, T. The Weak Hydrogen Bond: IUCr Monographs on Crystallography; Oxford University Press: New York, 1999. (2) Papaefstathiou, G. S.; Tsohos, A. T.; Raptopoulou, C. P.; Terzis, A.; Psycharis, V.; Gatteschi, D.; Perlepes, S. P. Cryst. Growth Des. 2001, 1, 191. (3) Garcia-Baez, E. V.; Matinez-Martinez, F. J.; Hopfl, H.; PadillaMartinez, I. I. Cryst. Growth Des. 2003, 3, 35. (4) Janiak, C. J. Chem. Soc., Dalton Trans. 2000, 3885. (5) Blanchard, M. D.; Hughes, R. P.; Concolino, T. E.; Rheingold, A. L. Chem. Mater. 2000, 12, 1604. (6) Nelson, D. L.; Cox, M. M. Lehninger Principles of Biochemistry, 3rd ed.; Worth Publishers: New York, 2000. (7) Guckian, K. M.; Schweitzer, B. A.; Ren, R.X.-F.; Sheils, C. J.; Tahmassebi, D. C.; Kool, E. T. J. Am. Chem. Soc. 2000, 122, 2213. (8) Zhong, C. J.; Kwan, W. S. V.; Miller, L. L. Chem. Mater. 1992, 4, 1423. (9) Mayo, S. L.; Olafson, B. D.; Goddard, W. A., III J. Phys. Chem. 1990, 94, 8897. (10) Momany, F. A.; Carruthers, L. M.; McGuire, F. R.; Scheraga, H. A. J. Phys. Chem. 1974, 78, 1595. (11) Sarma, J. A. R. P.; Desiraju, G. R. Cryst. Growth Des. 2002, 2, 93. (12) Lewis, F. D.; Liu, X.; Miller, S. E.; Wasielewski, M. R. J. Am. Chem. Soc. 1999, 121, 9746. (13) Zhong, C. J.; Kwan, W. S. V.; Miller, L. L. Chem. Mater. 1992, 4, 1423. (14) Chen, E. S.; Chen, E. C. M. Bioelectrochnol. Bioenerg. 1998, 46, 15. (15) Hunter, C. A.; Sanders, J. K. M. J. Am. Chem. Soc. 1990, 112, 5525. (16) Hunter, C. A. Angew. Chem., Int. Ed. Engl. 1993, 32, 1584. (17) Price, S. L.; Stone, A. J. J. Chem. Phys. 1987, 86, 2859. (18) Kurita, N.; Araki, M.; Nakao, K.; Kobayashi, K. Chem. Phys. Lett. 1999, 313, 693. (19) Sponer, J.; Hobza, P. Chem. Phys. Lett. 1997, 267, 263. (20) Glowka, M. L.; Martynowski, D.; Kozlowska, K. J. Mol. Struct. 1999, 474, 81. (21) Coppens, P. X-ray Charge Densities and Chemical Bonding; Oxford University Press: Oxford, 1997. (22) Hansen, N. K.; Coppens, P. Acta Crystallogr. 1978, A34, 909. (23) Koritsanszky, T. S.; Howard, S.; Macchi, P.; Gatti, C.; Farrugia, L. J.; Mallinson, P. R.; Volkov, A.; Su, Z.; Richter, T.; Hansen, N. K. XD (version 4.10, July), a computer program package for multipole refinement and analysis of electron densities from diffraction data; Free University of Berlin, Germany; University of Wales, Cardiff, U.K.; Universita di Milano, Italy; CNR-ISTM, Milano, Italy; University of

addition to the above-mentioned data55,56 we considered intermolecular N−H···N and N−H···O contacts for derivatives with DNA bases,57,58 adenine hydrates,59 and hydrates and dimers of several organic acids.60 The obtained graph demonstrates the same exponential dependence for values of electron density versus hydrogen bond distances for all common hydrogen bonds (N−H···N, N−H···O, O−H···N, O−H···O). It is noteworthy that all types of interactions starting from weak interactions to covalent bonds (O−H, N− H) fit this curve, as was already mentioned.56 Points corresponding to three hydrogen bonds obtained in our investigation are also in good agreement with this exponential dependence. Additionally we included in this graph other types of nonbonded interactions, obtained from the literature57,58 and from the current work. The most remarkable feature of this graph is that points corresponding to stacking interaction as well as contacts F···O and O···O are located above the line describing the exponential dependence. This fact points out that stacking interaction have the same nature as other specific intermolecular interactions like F···O, O···O; namely, all these interactions are mainly of van der Waals in nature.

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CONCLUSIONS The high-resolution low-temperature X-ray analysis was carried out for two furazan derivatives to investigate the electron density distribution in these compounds. It was shown that oxygen atoms of the furazan ring do not participate in the conjugation with the π-system. The results of topological analysis revealed that N−O bonds in the furazan ring should be described as close shell interaction, while the other intramolecular bonds are classical covalent bonds. The analysis of EDD in intermolecular area proved the presence of a stacking interaction between overlapping molecules. The character of electron density distribution in the overlapping area corresponds to the character of overlapping. The parameters of bond critical points revealed that such an interaction is close to specific interactions, for instance, O···O interaction. The energy of interaction calculated by topological analysis is 3.2−3.9 kcal/mol, which is comparable to 5426



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Glasgow, U.K.; State University of New York, Buffalo; University of Nancy, France, 2003. (24) Hirshfeld, F. L. Acta Crystallogr. 1976, A32, 239. (25) Bader, R. F. W. Atoms in Molecules: A Quantum Theory; Clarendon Press: Oxford, 1990. (26) Tsirelson, V. G.; Ozerov, R. P. Electron Density and Bonding in Crystals; IOP: Bristol and Philadelphia, 1996. (27) Abramov, Y. A.; Volkov, A.; Wu, G.; Coppens, P. J. Phys. Chem. B 2000, 104, 2183. (28) Gavezzotti, A. J. Phys. Chem. B 2002, 106, 4145. (29) Gavezzotti, A. J. Phys. Chem. B 2003, 107, 2344. (30) Espinosa, E.; Molins, E.; Lecomte, C. Chem. Phys. Lett. 1998, 285, 170. (31) Kirzhnits, D. A. Sov. Phys. JETP 1957, 5, 64. (32) Abramov, Yu. A. Acta Crystallogr. 1997, A53, 264. (33) Tsirelson, V.; Stash, A. Chem. Phys. Lett. 2002, 351, 142. (34) Lyssenko, K. A.; Antipin, M. Yu.; Antonov, D. Yu. ChemPhysChem 2003, 4, 817. (35) Konovalova, I. S.; Nelyubina, Y. V.; Lyssenko, K. A.; Paponov, B. V.; Shishkin, O. V. J. Phys. Chem. A 2011, 115, 8550. (36) Shishkina, A. V.; Zhurov, V. V.; Stash, A. I.; Vener, M. V.; Pinkerton, A. A.; Tsirelson, V. G. Cryst. Growth Des. 2013, 13, 816. (37) Sheremetev, A. B.; Yudin, I. L. Mendeleev Commun. 1996, 247. (38) (a) Starchenkov, I. B.; Andrianov, V. G. Khim. Geterotsikl. Soedin. 1996, 717; in Russian (b) Chem. Heterocycl. Compd. (Engl. Transl.) 1996, 32, 618. (39) (a) Starchenkov, I. B.; Andrianov, V. G.; Mishnev, A. F. Khim. Geterotsikl. Soedin. 1997, 250; in Russian (b) Chem. Heterocycl. Compd. (Engl. Transl.) 1997, 33, 216. (40) Bruker, SMART (v 5.051) and SAINT (v 5.00), Area Detector Control and Integration Software; Bruker AXS Inc.; Madison, Wisconsin, USA, 1998. (41) Sheldrick, G. M. SADABS; Bruker AXS Inc.; Madison, Wisconsin, USA, 1998. (42) Sheldrick, G. M. SHELXTL, v 5.1; Bruker AXS Inc.; Madison, Wisconsin, USA, 1998. (43) Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A., Jr.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian 03, Revision C.01; Gaussian, Inc.: Wallingford, CT, 2004. (44) Stash, A.; Tsirelson, V. J. Appl. Crystallogr. 2002, 35, 371. (45) Allen, F. H.; Kennard, O.; Watson, D. G.; Brammer, L.; Orpen, A. G.; Taylor, R. J. Chem. Soc., Perkin Trans. 1987, 2, S1. (46) Allen, F. H. Acta Crystallogr. B 2002, 58, 380. (47) Batsanov, A. S.; Struchkov, Yu.T. Zh. Strukt. Khim. 1985, 26, 65. (48) Averkiev, B. B.; Antipin, M. Y.; Sheremetev, A. B.; Timofeeva, T. V. Acta Crystallogr. 2003, C59, o383. (49) Suponitsky, K. Yu.; Lyssenko, K. A.; Antipin, M. Yu.; Aleksandrova, N. S.; Sheremetev, A. B.; Novikova, T. S. Russ. Chem. Bull. 2009, 58, 2129. (50) Suponitsky, K. Yu.; Masunov, A. E.; Antipin, M. Yu. Mendeleev Commun. 2009, 19, 311. (51) Sheremetev, A. B.; Kozeev, A. M.; Aleksandrova, N. S.; Struchkova, M. I.; Suponitsky, K. Yu. Chem. Heterocycl. Compd. 2013, 49, 1358.

(52) Palysaeva, N. V.; Kumpan, K. P.; Struchkova, M. I.; Dalinger, I. L.; Kormanov, A. V.; Aleksandrova, N. S.; Chernyshev, V. M.; Pyreu, D. F.; Suponitsky, K. Yu.; Sheremetev, A. B. Org. Lett. 2014, 16, 406. (53) Rowland, R. S.; Taylor, R. J. Phys. Chem. 1996, 100, 7384. (54) Lyssenko, K. A.; Antipin, M.Yu. Russ. Chem. Bull., Int. Ed. 2004, 53, 10. (55) Peters, M.; Rozas, I.; Alkorta, I.; Elguero, J. J. Phys. Chem. B 2003, 107, 323. (56) Mallinson, P. R.; Smith, G. T.; Wilson, C. C.; Grech, E.; Wozniak, K. J. Am. Chem. Soc. 2003, 125, 4259. (57) Gu, J.; Wang, J.; Leszczynski, J. J. Phys. Chem. B 2004, 108, 9277. (58) Gu, J.; Wang, J.; Leszczynski, J. J. Phys. Chem. B 2004, 108, 8017. (59) Sukhanov, O. S.; Shishkin, O. V.; Gorb, L.; Podolyan, Y.; Leszczynski, J. J. Phys. Chem. B 2003, 107, 2846. (60) Ranganathan, A.; Kulkarni, G. U.; Rao, C. N. R. J. Phys. Chem. A 2003, 107, 6073.

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Experimental X-ray Diffraction Study of Stacking Interaction in Crystals

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