Research Article Electron Charge Density Distribution from X-Ray Diffraction Study of the 4-Methoxybenzenecarbothioamide Compound

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1 Crstallograph Volume 2013, Article ID , 7 pages Research Article Electron Charge Densit Distribution from X-Ra Diffraction Stud of the 4-Methobenzenecarbothioamide Compound Mokhtaria Drissi, Abdelkader Chouaih, Youcef Megrouss, and Fodil Hamzaoui Laboratoire de Technologie et Propriétés du Solide (LTPS), Faculté des Sciences et de la Technologie, UniversitéAbdelhamidIbnBadisdeMostaganem,27000Mostaganem,Algeria Correspondence should be addressed to Abdelkader Chouaih; achouaih@gmail.com Received 31 March 2013; Accepted 1 Jul 2013 Academic Editors: N. Ishii and E. Suresh Copright 2013 Mokhtaria Drissi et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in an medium, provided the original work is properl cited. The molecular electron charge densit distribution of the title compound is described accuratel using the multipolar model of Hansen and Coppens. The net atomic charge and the in-crstal molecular dipole moment have been determined in order to understand the nature of inter- and intramolecular charge transfer. The stud reveals the nature of intermolecular interactions including charge transfer and hdrogen bonds in the title compound. In this crstal, the molecules form dimers via N H S intermolecular hdrogen bonds. The dimers are further linked b C H O hdrogen bonds into chains along the c crstallographic ais. This stud has also allowed us to determine the electrostatic potential and therefore locate the electropositive part and the electronegative part in molecular scale of the title compound. 1. Introduction The chemistr of thioamides and their derivatives continues to be of particular interest due to their interesting structural features and also due to their biological importance. Heterocclic compounds of these tpes ehibit a wide spectrum of biological activit and have etensive practical applications [1 3]. In addition, thioamides are important ligands in the field of coordination chemistr [4]. Due to these positive traits, thioamides have been under stud for a long time, but much of their basic chemistr remains uneplored. The heterocclic 4-methobenzenecarbothioamide compound, of chemical formula C 8 H 9 NOS, crstallizes in the P space group, with eight molecules in the unit cell. The general features of the structure have been described previousl [5]. It contains two independent molecules with the metho groups oriented in opposite conformations. The mean planes of the carbothioamide groups are tilted b 7.88(15) and (9) from the mean planes of the benzene rings. In this work, the crstallographic data were taken from another article [5]andusedforthecurrentstud.Thestructure has been redetermined using the same X-ra diffraction data. So this work focuses on the thermal analsis and electronic charge densit stud of the 4-methobenzenecarbothioamide molecule. The scope of this stud is to model aspherical features of the atomic electron densit arising from chemical bonding at low temperature of the molecule b transferring the electron densit multipole parameters obtained from accurate X-ra diffraction eperiments and calculate the molecular dipole moment. In order to understand the nature of inter- and intramolecular charge transfer, the electrostatic potential distribution of the molecule in crstal has been analzed. 2. Materials and Methods 2.1. High-Order Spherical Atom Refinement. A high-order spherical atom refinement (HO) on the non-h atoms is performed to get least-biased positional and thermal parameters. Hence, due to the properties of the Fourier transform, this HO procedure refines the positional and anisotropic thermal motion parameters onl on core electrons. Because valence electron scattering factors diffuse onl at low resolution, HO refinement gives precise positions and displacements of the core electrons onl.

2 2 Crstallograph In order to etract the aspherical features of the electron densit, the following strateg was designed. First, a fullanisotropic spherical atom refinement using starting parameters from a Shell [6] refinement is performed. Then, the multipole refinement which has been developed b Hansen and Coppens [7] is selected to perform the electron densit analsis using the MoPro package software [8]. In parallel, the net atomic charge on the different atoms of the title compound and the molecular dipole moment were also estimated b theoretical calculations. Theoretical calculations were performed with the Gaussian package [9] at the HF/6-31G level of theor and semiempirical methods. A higher-order refinement of X-ra data becomes essential to obtain accurate core positions and the associated thermal parameters of the different atoms of the molecule. TheX-rascatteringfactorsforS,C,N,andOatoms come from the international tables for X-ra crstallograph [10] while for H atom the bonded H-atom scattering curve of Stewart et al. (1965) was used [11]. The H atoms were found b difference Fourier snthesis and their coordinates were adjusted b etending along the C H and N H bond directions to bond lengths of Åand1.020Å, respectivel. An position error of the hdrogen atom will bring about errors strongl correlated with the dipolar population of hdrogen. Refinement details are displaed in Table Charge Densit Multipole Model. The Hansen-Coppens multipole formalism, as implemented in the Mopro leastsquares program for multipole refinement, was used for both observed and theoretical structure factor fitting. It describes the crstal electron densit as a superposition of aspherical pseudo-atoms each modeled on a multipole epansion: ρ atom ( r) =ρ c ( r) +P V K 3 ρ V (k r) l ma + l +1 m= 1 K R l (K r) P lm Y lm ( r (1) r ). Here ρ c and ρ V are sphericall averaged Hartree-Fock core and valence densities, with ρ V being normalized to one electron. The Slater-tpe radial functions R l ( r) = N l r n l l ep( k ξ l r) modulate the spherical harmonic angular functions Y lm± and N 1 is a normalization factor. The values for parameters n=n 1 and ξ were chosen according to rules provided b Coppens (1997) [12]. In practice, two charge densit variables, the population parameter and a kappa parameter which allows epansion and contraction of the valence shell, are added to the conventional parameters of structure analsis [13]. The population parameters P V and P lm are floated along with κ and κ during the refinement. The sum over m in (1) includes ±l, so that for each one, 2l +1 functions are included. The aspheric charge densit was describedattheoctupolelevel(l=3)fortheatomsc,n,and O and the headecapole for the atoms S (l =4)andatthe dipole levels (l =1or 2) for hdrogen atoms not involved and involved in strong H bonds, respectivel. Charge densities of all hdrogen were considered to have clindrical smmetr along the corresponding hdrogen-heav atom bond. Table 1: Refinement details. N R wr Spherical refinement Multipole refinement Wavelength, λ (Å) Completeness (%) 99.4 Resolution, Sinθ/λ (Å 1 ) 0.8 N is the number of refined parameters. R = F o F c / F o ; wr = [ w( F o F c ) 2 / w F o 2 ] 1/2. H8B z z z z z Figure 1: Labeling of the atoms and definition of local orthogonal reference aes for the atom-centered multipolar functions. Table 2: Matri for differences in MSDAs (mean square displacements of atoms) (values listed are 10 4 MSDAs for column atom minus that for row atom; values correspond to chemical bonds). Molecule A Molecule B 4 3 C9 5 2 S2 42 N The qualit of a refined model can be monitored based ontheresidualsandthegoodnessoffitapartfromclosel inspecting the deformation densit maps. This model provides the advantage of using constraints based on assumed localsmmetrontheatomicsitestolimitthenumberof

3 Crstallograph 3 Table 3: Rigid-bod motion parameters. L (rad 2 ) T (Å 2 ) S (rad Å) ( ) ( ) ( ) Table 4: Net charges (q) in the different atoms of the title compound. Atoms q Eperimental Ab initio Semiempirical H8B least-squares variables. Figure 1 gives the local site smmetr of the different atoms of the molecule. 3. Results and Discussion 3.1. Structural and Thermal Vibration Analsis. The main characteristic of this structure is that the eight molecules in the unit cell are engaged in seven chains formed b infinite chains of hdrogen-bonded coplanar molecules. The different chains link translationall equivalent molecules along the c crstallographic ais through C S and N H bonds. The rigid bond test indicated that the differences between the mean square displacements amplitudes (MSDAs) along interatomic directions have magnitudes Δ Å 2 for nearl all the bonded pairs of the non-h atoms [14]. In contrast, along intramolecular interatomic directions some Δ values were considerabl larger, indicating that the molecule is not entirel rigid and that low-frequenc soft modes of internal molecular vibration contribute significant1 to the observed mean square displacements[15]. The thermal motion analsis of the title compound has been performed H8B Figure 2: ORTEPIII diagram of the title compound. Thermal ellipsoids are shown for the 30% probabilit level. using the THMA11 program [16]. Selected results are presented intable 2. The rigid-bod motion is described b three tensors T, L, and S taking into account translation, liberation, and the correlation between translation and liberation, of the rigid group, respectivel. These tensors are obtained b a leastsquares fit refinement using the observed atomic thermal motion parameters obtained b the refinement. In terms of rigid-bod TLS, thecalculatedanisotropic thermal parameters are given in the Trueblood notation as such: U ij =T ij +G ijkl L kl +H ijkl S kl +D 2 Ω 2 n i n j, (2) where G and H are geometrical parameters. The analsis of the non-h atoms in terms of rigid-bod motion ields the T, L, ands tensor values summarized in Table 3.Theellipsoids of the different atoms representing their thermal motion described before are shown with an ORTEPIII diagram [17] in Figure Electron Densit Maps. The aspherical atom model used in multipole refinement gives structure factor phases closer to the true phases for crstals than the spherical or independent atom model does. This enables the mapping of the electron densit b the Fourier snthesis in various was using the WinGX program [18] to represent the eperimental densit deformation and the VMoPro program, implemented in the MoPro package, to observe the dnamic densit deformation of the molecule. The residual map using a spherical atom model is shown in Figure 3, fromwhichwecannoticetheabsenceofthe densit on the atomic sites and the appearance of all the bond densit peaks. This map confirms the high qualit of the data

4 4 Crstallograph Table 5: Components of the dipolar moment of the charge distribution from the point charge models (AM1 and B3LYP/6-31G )and comparison with the components derived from eperimental electron densit (multipolar refinement). Methods Models μ μ μ z μ (Debe) X-Ra eperiment Multipolar refinement Semiempirical AM Ab initio B3LYP/6-31G qualit of the recorded data and the precision of the used equipment. Figure 3: Eperimental densit map from high-order refinement. Contour map is 0.06 e Å 3. sets and the efficienc of the formalism used for the data processing as proposed b Blessing [19]. The final electron densit deformation was calculated using the following equation: Δρ dn ( r) = 1 V H [ F mul ( H) eiφ mul( H) F sph ( H) eiφ sph( H) ]e i2π H r. This map is obtained from the calculated multipole structure factors F mul (H), where F sph (H) is computed with atomic positions and thermal parameters obtained from the multipole refinement. Figure 4 shows this electron densit deformation on the different atoms in the benzene ring section of the title compound,whereonecaneasilobservetheobviousincrease of the densit and the good localization peaks in the middle of covalent bonds of the ccle of the molecule. In Figure 5, the densit map contains two independent molecules A and B. The densit maps are given in the two representations of the metho groups. Figure 6(a) shows the densit deformation at the plane z and Figure 6(b) the deformation in the plane. A residual densit map in the molecular plane obtained in the final ccle of multipole refinement (see Figure 7) shows the adequac of the multipolar model to describe the electron eperimental densit of the molecule. The quasitotalit absence of the densit peaks again confirms the high (3) 3.3. Hdrogen Bond. Hdrogen bonds can be classified on thebasisofchargedensit.thecrstalstructureofthetitle compoundrestsonchainsofmoleculejoinedbhdrogen bonds. The almost linear hdrogen bonding links b translationof equivalentmolecules along thec crstallographic ais in the unit cell. In this crstal, the molecules form dimers via intermolecular N H S intermolecular hdrogen bonds. The dimers are further linked b C H O hdrogen bonds into chains along the c-ais. Figure 8 shows the electron densit in the plane of the hdrogen bonds formed b the atoms (N2, H2B, and ), eisting in the molecule. The electron densit in the intermolecular hdrogen bonds is deficient in charge between the donor and acceptor of the molecule Net Atomic Charges. Knowledge of the charge densit function can lead to some important properties of the molecule such as the net charges on the different atoms, the molecular dipole moment, and the electrostatic potential around the molecule. The valence population coefficients P i V were used to estimate the partial charges on the different atoms according to the following equation: q i =n i P i V, (4) where n i is the total number of electrons of atoms i. The population coefficients are presented in Table 4.Therefined atomic charges are generall of the sign epected from chemical knowledge: H atoms are positivel charged, whereas O, S, and N atoms are negativel charged. The net atomic charges obtained b the X-ra eperimental method using themultipolarmodelarecomparedtothosederivedfrom the theoretical calculations. Semiempirical calculations were carried out using the AM1 (Austin s method) and ab initio calculations were carried out at the HF/6-31G levels of theor using the Gaussian package. The results obtained b both theor and eperiment methods are summarized in Table 4. The eperimental results and those derived from the semiempirical and ab initio calculations are in good agreementconcerningthesignsofthenetchargesoftheh atoms and those of the N, S, and O atoms.

5 Crstallograph 5 H8B H14 H16B H16C 6 S2 H O2 C9 1 2 H12 H2B N2 H2A H11 H16A Molecule A (a) (b) Molecule B Figure 4: Dnamic densit maps of the two molecules A and B with the metho groups oriented in opposite conformations of the title compound. Contour map is 0.05 e Å 3. H2B S2 H15 H2B N2 H2A C9 H Figure 5: Dnamic densit map in the plane (,, and ) contains two independent molecules A and B. Contour map is 0.05 e Å Molecular Dipole Moment. The molecular dipole moment was first estimated using the population coefficients of the multipolar densit model from the following equation: μ= i q i r i + i 4n + 3 3k i (P i i+p i j+p zi k), (5) where r i is the atomic position and n is the number of electrons in the molecule. P i are the dipolar electron populations. Dipole moment orientation in the molecule is shown in Figure 9. The resulting molecular dipole moment direction is in accordance with the evaluation of the positive sign of the net charges on the H atoms and the negative sign of the net charges on the O, S, and N atoms. In a parallel stud, the net charges on the different atoms andthemoleculardipolemomentwerealsoestimatedb ab initio (B3LYP/6-31G ) and semiempirical (AM1) calculations. In this procedure the treatment is confined to the valence-shell electrons. The results of these calculations are presented in Table 5. From the results, we can see a good agreement between the value obtained with X-ra diffraction ( D) and the other values obtained b theoretical calculation (AM1 gives D and DFT gives D). Analsis of obtained dipole moments shows that the size and direction of the dipole moment vector depend mainl on the position of substituents. Furthermore, the orientation of thedipolemomentvectoristowardthesulfuratom Electrostatic Potential. The distribution of positive and negative charges in a crstal full defines phsical properties liketheelectrostaticpotentialanditsderivatives.theelectrostatic potential is important in the stud of intermolecular interactions of molecular sstems. For a continuous charge distribution stud, the potential is obtained b integration over the space containing the distribution. At a point defined b r,thepotentialingiven b φ (r ) = ρ total(r) dr. (6) r r In which ρ total represents both the nuclear and the electronic charge, where the integration is over the molecular volume,

6 6 Crstallograph H16A H16C 6 H8B H16B (a) (b) Figure 6: Dnamic densit map of the metho groups: (a) deformation in the plane of the molecule A; (b) deformation in the plane of the molecule B. Contour map is 0.05 e Å 3. S2 H2B H15 C9 N2 H2A Figure8:Deformationdensitmapintheplaneofthehdrogen bond formed b the atoms (N2, H2B, and ). Contour map is 0.05 e Å 3. Figure 7: Residual densit map: ρ res =ρ 0 ρ mult. Contour map is 0.05 e Å 3. and r represents the atomic position relative to common origin. The integration includes the atoms of onl one molecule and therefore does not include directl the effects of charge distribution of the neighboring molecules. Figure 10 shows the electrostatic potential distribution in the plane of the base ring. The etension of the positive electrostatic potential around the carbothioamide and C H groups and the regions of negative electrostatic potential around the nitro and hdrol groups confirm the nature of theintramolecularchargetransferasfoundbtheorientation of the molecular dipole moment. The obtained point charges corresponding to S atom are 0.332, 0.250, and e from eperimental, ab initio, and semiempirical methods, respectivel. But the region ver close to S appears positive. This is because of the fact that S atom of the title compound is surrounded b the most electropositive hdrogen atoms ( = 0.017, = 0.017, = 0.019, and = e). 4. Conclusion Thisstudhasobtainedgoodaccurateresultsonthestructure which gives high-qualit descriptive model for the electron charge densit distribution from X-ra diffraction eperiment. It also shows that electron densit can ield electronic proprieties such as dipole moment. Its determination lets us locatetheregionofthedonorandtheacceptorgroupsand also the direction of charge transfer within the molecule. The deformation of the electrostatic potential of the title compound shows that the electronegative potential is located on the side of metho group and electropositive potential is on the side of carbothioamide group. In the multipole refinement, all nonhdrogen atoms were refined anisotropicall and subject to a rigid-bond constraint. H atoms anisotropic parameters are obtained from TLS

7 Crstallograph 7 μ S μ A μm Figure 9: Orientation of the molecular dipole moment of the title compound; the origin is at the center of mass of the molecule; μ M : molecular dipole moment from the multipolar model; μ S :molecular dipole moment from the semiempirical calculation; μ A :molecular dipole moment from the ab initio calculation. H8B Figure10:Theelectrostaticpotentialmapsaroundthemolecule. The section is in the plane of the benzene ring. analsis. The final R factor (2.2%) attests to the qualit of the data. To stud the effect of electron charge transfer in biological activit more, we should perform vibrational analsis using FT-Raman and FTIR spectroscopic techniques. References z [5]S.Ali,S.Hameed,A.Luqman,T.Akhtar,andM.Parvez, 4- Methobenzenecarbothioamide, Acta Crstallographica Section E,vol.66,no.6,p.o1272,2010. [6] G. M. Sheldrick, SHELXL97: Program for Crstal Structure Determination, Universit of Gttingen, Göttingen, German, [7] N. K. Hansen and P. Coppens, Testing aspherical atom refinements on small-molecule data sets, Acta Crstallographica A, vol. 34, pp , [8]C.Jelsch,B.Guillot,A.Lagoutte,andC.Lecomte, Advances in protein and small-molecule charge-densit refinement methods using MoPro, Applied Crstallograph, vol.38, no. 1, pp , [9] M.J.Frisch,G.W.Trucks,H.B.Schlegeletal.,GAUSSIAN-03, Revision E.01, Gaussian, Wallingford, UK, [10]E.PrinceandA.J.C.Wilson,International Tables for X-Ra Crstallograph, vol. C, Kluwer Academic, Boston, Mass, USA, 2nd edition, [11] R. F. Stewart, E. R. Davidson, and W. T. Simpson, Coherent X- ra scattering for the hdrogen atom in the hdrogen molecule, The Chemical Phsics, vol.42,no.9,pp , [12] P. Coppens, X-Ra Charge Densities and Chemical Bonding, Oford,NewYork,NY,USA,1997. [13] M. A. Spackman, 5 Charge densities from X-ra diffraction data, Annual Reports on the Progress of Chemistr C, vol.94, pp , [14] F. L. Hirshfeld, Can X-ra data distinguish bonding effects from vibrational smearing? Acta Crstallographica A, vol. 32, pp , [15] R.E.Rosenfield,K.N.Trueblood,andJ.D.Dunitz, Atestfor rigid-bod vibrations based on a generalization of Hirshfeld s rigid-bond postulate, Acta Crstallographica A, vol. 34, pp , [16] K. N. Trueblood, THMA11 Program, Department of chemistr and biochemistr, Universit of California, Los Angeles, Calif, USA, [17] L. J. Farrugia, ORTEP-3 for windows a version of ORTEP- III with a graphical user interface (GUI), Applied Crstallograph,vol.30,no.5,p.565,1997. [18] L. J. Farrugia, WinGX suite for small-molecule single-crstal crstallograph, Applied Crstallograph,vol.32,no. 4, pp , [19] R. H. Blessing, Outlier treatment in data merging, Applied Crstallograph, vol. 30, no. 4, pp , [1] H. Quiniou and O. Guillton, 1,3-Thiazines, in Advances in Heterocclic Chemistr,A.R.Katritzk,Ed.,vol.50,pp , Elsevier, San Diego, Calif, USA, [2] S. P. Singh, S. S. Parmar, K. Raman, and V. I. Stenberg, Chemistr and biological activit of thiazolidinones, Chemical Reviews,vol.81,no.2,pp ,1981. [3] M. D. Mashkovskii, Drugs, Torsing, vol. 2, p. 244, 1998 (Russian). [4] S. T. Lebana, R. Sultana, and G. Hendal, Heterocclic thioamides of copper(i): snthesis and crstal structures of copper complees with 1,3-imidazoline-2-thiones in the presence of triphenl phosphine, Polhedron, vol. 27, no. 3, pp , 2008.

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