synthesis and crystal structure of 1-(4-nitrobenzyl)-3...

Hindawi Publishing CorporationJournal of ChemistryVolume 2013 Article ID 603579 8 pageshttpdxdoiorg1011552013603579

Research ArticleSynthesis and Crystal Structure of1-(4-Nitrobenzyl)-3-allyl-1H-benzo[d]imidazol-2(3H)-one

Dounia Belaziz1 Santiago V Luis2 Youssef Kandri Rodi1

Ineacutes Martiacute2 and Vicente Martiacute-Centelles2

1 Laboratoire de ChimieOrganiqueAppliquee Faculte des Sciences et Techniques Universite SidiMohamedBenAbdallah FesMorocco2Universitat Jaume I Departamento de Quımica Inorganica y Organica Avenida Sos Baynat sn E-12071 Castellon Spain

Correspondence should be addressed to Santiago V Luis luissqioujies and Youssef Kandri Rodi youssef kandri rodiyahoofr

Received 29 May 2013 Accepted 2 July 2013

Academic Editor Veysel T Yilmaz

Copyright copy 2013 Dounia Belaziz et alThis is an open access article distributed under the Creative Commons Attribution Licensewhich permits unrestricted use distribution and reproduction in any medium provided the original work is properly cited

A functionalized benzimidazole 1-(4-nitrobenzyl)-3-allyl-1H-benzo[d]imidazol-2(3H)-one has been synthesized and the crystalstructure was determined and analyzed This compound crystallizes in the monoclinic space group P2

1n (number 14) c with

cell parameters 119886 = 712148(8) A 119887 = 1612035(17) A 119888 = 1304169(17) A 120573 = 933043(11) 119881 = 149471(3) A3 and 119863calc =1375 gmm3 The solid state geometry is stabilized by intermolecular 120587ndash120587 interactions along with the van der Waals interactionswhich contribute to the stability of the crystal packing Computational calculations have been used to properly understand themain intermolecular interactions present in the crystal

1 Introduction

Functionalized benzimidazoles represent an important classof N-containing heterocyclic compounds and have receivedconsiderable attention in recent times because of their appli-cations as antiulcer antihypertensive antiviral antifungalanticancer and antihistamine activities among others [1ndash5]They are important intermediates in many organic reactions[6 7] and act as ligands to transition metals for modellingbiological systems [8 9] In addition the effectiveness ofbenzimidazoles in the treatment of diseases such as ischemia-reperfusion injury [10] hypertension [11] and obesity [12] hasbeen recently reported Owing to their potential biologicalactivities and other possible applications of the benzimida-zoles a clear need exists for developing synthetic strategiesfor the preparation of substituted benzimidazoles

As a continuation of our research work devoted to thedevelopment of substituted benzimidazol-2-one derivatives[13ndash15] here we report on the synthesis of a new benzimid-azol-2-one derivative displaying a new substitution pattern

This compound has been obtained by the reaction of allyl-bromide (4) with 1-(4-nitrobenzyl)-1H-benzo[d]imidazol-2(3H)-one (3) in the presence of a catalytic quantity of tetra-n-butylammonium bromide under mild conditions provid-ing the disubstituted compound (5) (Scheme 1)

2 Materials and Methods

To 1H-benzo[d]imidazol-2(3H)-one (1) (030 g 224mmol)potassium carbonate (037 g 268mmol) and tetra-n-butylammonium bromide (007 g 022mmol) in DMF(20mL) were added to 4-nitro-benzylbromide (2) (058 g268mmol) Stirring was continued at room temperaturefor 6 hours The salt was removed by filtration and thefiltrate concentrated under reduced pressure The obtainedcompound (3) 1-(4-nitrobenzyl)-1H-benzo[d]imidazol-2(3H)-one was separated by chromatography on a columnof silica gel with ethyl acetatehexane (1 2) as eluent Thecompound was recrystallized from ethanol to give colorlesscrystals (Scheme 2)

2 Journal of Chemistry

C11

C9C13

C10

C12

C14

N3N2

C8

O3

C17C16 C15

C4

C7

C3

C5 C6

O1C2

N1

O2

C1

Figure 1 ORTEP representation of 5 (displacement ellipsoids are drawn at the 50 probability level)

Figure 2 The unique molecule in the crystal structure of 5 (displacement ellipsoids are drawn at the 50 probability level)

(5)

N

N

O

NO2

Scheme 1

To the formerly obtained compound (3) (017 g 063mmol) allylbromide (4) (009 g 076mmol) in DMF (10mL)potassium carbonate (010 g 076mmol) and tetra-n-buty-lammonium bromide (002 g 0063mmol) were added(Scheme 3) Stirring was continued at room temperature for12 hours The salt was removed by filtration and the filtrateconcentrated under reduced pressure The residue was sep-arated by chromatography on a silica gel column with ethylacetatehexane (1 1) as the eluent The obtained compound(5) was recrystallized from dichloromethanehexane to givecolorless crystals of 5 (melting point = 95∘C yield = 87)

Single crystals of 5 were obtained from dichlorometh-anehexane to give colorless crystals A suitable crystalwas selected and measured on an Agilent SuperNova Atlas

Dual Source Agilent Technologies diffractometer using theCrysAlisPro softwareThe crystal was kept at 20000K duringdata collection Using Olex2 [16] the structure was solvedwith the ShelXS [17] structure solution program using directmethods and refined with the ShelXL [17] refinement pack-age using least squares minimization All hydrogen atomswere fixed in geometrical positions Nonhydrogen atomswere refined with anisotropic displacement parameters Themolecular connectivity and the crystal packing diagramweredrawn using the Mercury (CCDC) program [18] and PyMol[19] Geometrical measurements were carried out using theMercury (CCDC) program [18]

Crystal Data for 5 C17H15N3O3(M = 30932) mon-

oclinic space group P21n (no 14) a = 712148(8) A b

= 1612035(17) A c = 1304169(17) A 120573 = 933043(11) V= 149471(3) A3 Z = 4 T = 20000(10) K 120583(Cu K120572) =0795mmminus1119863calc = 1375 gmm3 14200 reflections measured(874 le 2Θ le 14606) 2935 unique (119877int = 00215) which wereused in all calculationsThe final 119877

1was 00353 (gt2sigma(I))

and wR2was 00962 (all data) CCDC number 948080 See

Figure 1 for the ORTEP representation of 5In order to obtain an additional insight into the inter-

molecular forces determining the crystal packing compu-tational calculations were used for the optimization of themolecule and the calculation of the energies associated tothe different intermolecular interactions at the PM3 level ofcalculation using the Spartanrsquo08 software [20]

Journal of Chemistry 3

NH

NHO

NH

NO

BTBADMFrt

Br

(1) (2) (3)7012eq

K2CO3

NO2

NO2

+

Scheme 2

NH

NO

Br N

NO+

BTBADMFrt

12eq 87(3) (4) (5)

K2CO3

NO2NO2

Scheme 3

Figure 3 Superimposed structures optimized at PM3 red X-raygreen

3 Results and Discussion

The details of the crystal data data collection and structurerefinements are shown in Table 1 and the unique molecule inthe crystal structure of 5 in Figure 2

The title compound C17H15N3O3is a new heterocyclic

system deriving from 1H-benzo[d]imidazol-2(3H)-one Thecrystal structure of this molecule is formed by two fusedsix- and five-membered rings linked to one benzyl andone allyl groups The fused-ring system is fundamentallyplanar with the maximum deviation from the mean planeof 0010 (6) A for N3 The benzyl and allyl groups are almostperpendicular to the benzimidazole plane but oriented inopposite directions (Figure 2)

Table 1 Crystal data and structure refinement for 5

Empirical formula C17H15N3O3

Formula weight 30932TemperatureK 20000(10)Crystal system MonoclinicSpace group P21n119886A 712148(8)119887A 1612035(17)119888A 1304169(17)120572∘ 9000120573∘ 933043(11)120574∘ 9000VolumeA3 149471(3)119885 4119863calcmgmm3 1375mmmminus1 0795119865(000) 6480Crystal sizemm3 0225 times 01759 times 0072Θ range for data collection 874 to 14606

Index ranges minus8 le ℎ le 8 minus20 le 119896 le 19 minus13le 119897 le 16

Reflections collected 14200Independent reflections 2935[119877(int) = 00215]Datarestraintsparameters 29350216Goodness-of-fit on 1198652 1070Final 119877 indexes [119868 ge 2120590 (119868)] 119877

1= 00353 119908119877

2= 00930

Final 119877 indexes [all data] 1198771= 00394 119908119877

2= 00962

Largest diff peakholee Aminus3 018minus023

The theoretical PM3 calculations after geometrical opti-mization of the molecule reveal torsion angles and these


36103005

3703

Figure 4 Intermolecular 1H-benzo[d]imidazol-2(3H)-onendash1H-benzo[d]imidazol-2(3H)-one 120587ndash120587 interactions

3610

3703

3610

Figure 5 Arrays formed by intermolecular 1H-benzo[d]imidazol-2(3H)-onendash1H-benzo[d]imidazol-2(3H)-one 120587ndash120587 interactions

3733

Figure 6 Intermolecular 120587ndash120587 interactions

have been compared with the experimental values Thetorsion angles of the 1H-benzo[d]imidazol-2(3H)-one sub-stituents of the calculated geometry differ significantly fromthe ones obtained in the solid state structure (Figure 2) TheC4ndashC7ndashN2ndashC8 angle changes from 10683(12)∘ in the solidstate to 7246∘ in the optimized geometry A similar trend isfound for the C16ndashC15ndashN3ndashC8 that has a value of 11184(13)∘in the solid state and 7256∘ in the optimized geometryThe variations in the bond angle are not as important N2ndashC7ndashC4 that has a value of 11152(10) in the solid state and

ao

c

b

Figure 7Molecular packing in the unit cell showing fourmoleculesin the asymmetric unit

11444∘ in the optimized geometry N3ndashC15ndashC16 that hasa value of 11265(10) in the solid state and 11391∘ in theoptimized geometry These results suggest that the change inthe conformation of themolecule will be stabilized by the for-mation of intermolecular interactions in the crystal structureovercoming the unfavorable conformational changes in thesubstituents Figure 3

An analysis of the crystal packing shows the pres-ence of intermolecular 120587ndash120587 interactions between the 1H-benzo[d]imidazol-2(3H)-one rings Two of those interac-tions can be observed in one of them the two moleculesdisplaying an L shape are oriented in an antiparallel arrange-ment while in the second one both molecules adopt a com-plementary disposition one siting over the other Figure 4 Inthis second case the benzene moiety of the benzoimidazolering of one molecule is pointing towards the nitrobenzenefragment of the secondmolecule with anH-centroid distanceof 3005 A a new Hndash120587 interaction is formed stabilizing theformation of such dimeric unitsThesemain interactions that


Figure 8 Observed arrays of parallel aromatic units involvingnitrobenzenendashnitrobenzene interactions (bc plane) highlighted ingreen and cyan

Figure 9 Observed arrays (based on nitrobenzenendashnitrobenzeneinteractions) highlighted in green and cyan in the bc plane and inthe a direction inmagenta (formed by 1H-benzo[d]imidazol-2(3H)-onendash1H-benzo[d]imidazol-2(3H)-on 120587ndash120587 interactions)

Table 2 Bond lengths for 5

Length (A)C1ndashC2 13810(16)C1ndashC6 13835(16)C1ndashN1 14653(15)C2ndashC3 13855(17)C3ndashC4 13894(17)C4ndashC5 13928(16)C4ndashC7 15147(16)C5ndashC6 13815(16)C7ndashN2 14534(16)C8ndashN2 13809(15)C8ndashN3 13778(17)C8ndashO3 12255(15)C9ndashC10 13809(16)C9ndashC14 13974(17)C9ndashN2 13885(15)C10ndashC11 13908(18)C11ndashC12 13869(19)C12ndashC13 13923(17)C13ndashC14 13801(17)C14ndashN3 13898(14)C15ndashC16 14959(18)C15ndashN3 14551(15)C16ndashC17 1306(2)N1ndashO1 12241(15)N1ndashO2 12182(15)

held together the molecules of 5 have 3610 A and 3703 Acentroid-centroid distances see Figures 4 and 5 Thesedirectional interactions yield to the formation of orderedarrays of parallel 1H-benzo[d]imidazol-2(3H)-one

Intermolecular 120587ndash120587 interactions between the nitroben-zene substituents are also found in the crystal structurehaving a 3733 A centroid-centroid distance Figure 6 Theposition of the molecules in the asymmetric unit is depictedin Figure 7

Thus this arrangement generates parallel arrays ofnitrobenzene rings (bc plane) that are held together by120587ndash120587 interactions (Figure 8) along with arrays of parallelbenzimidazole fragments in the adirection also based on120587ndash120587interactions (Figure 9)

Computational studies at a semiempirical level of theoryPM3 (from X-ray geometries without optimization at PM3level of theory) allow obtaining the relative stability ofthe different 120587ndash120587 interactions observed in the solid statestructure (Figure 10) For this purpose the relative energyof the dimers displayed in Figure 10 each one containingone of such intermolecular interactions except the first onecontaining two was calculated with all the distances andangles fixed according to the X-ray structure Thus cal-culations predict that the 1H-benzo[d]imidazol-2(3H)-one-1H-benzo[d]imidazol-2(3H)-one 120587ndash120587 interaction is more


NN NN O2N

41357kcalmol 41413 kcalmol 41606 kcalmol

O2N

NO2NO2

O2N

NO2

NO

O

O

O

NO

NNNN O

NN

360 361 362 369 370 371 372 373 374 375

4135

4140

4145

4150

4155

4160

4165

PM3

ener

gy (k

calm

ol)

3610 A centroid-centroid 3703 A centroid-centroid 3733 A centroid-centroid

Centroid-centroid distance (A)

Figure 10 Calculated energy for the dimers observed at the X-ray crystal structure

HOMO

LUMO LUMO + 1 LUMO + 2

HOMO minus 1 HOMO minus 2

Figure 11 Frontier orbitals HF3-21Glowast from X-ray geometry


Table 3 Bond angles for 5

Angle (∘)C2ndashC1ndashC6 12280(11)C2ndashC1ndashN1 11825(10)C6ndashC1ndashN1 11892(10)C1ndashC2ndashC3 11824(11)C2ndashC3ndashC4 12066(11)C3ndashC4ndashC5 11933(10)C3ndashC4ndashC7 12098(11)C5ndashC4ndashC7 11967(11)C6ndashC5ndashC4 12107(11)C5ndashC6ndashC1 11788(10)N2ndashC7ndashC4 11152(10)N3ndashC8ndashN2 10621(10)O3ndashC8ndashN2 12665(12)O3ndashC8ndashN3 12714(12)C10ndashC9ndashC14 12151(11)C10ndashC9ndashN2 13152(11)N2ndashC9ndashC14 10697(10)C9ndashC10ndashC11 11710(11)C12ndashC11ndashC10 12132(11)C11ndashC12ndashC13 12163(12)C14ndashC13ndashC12 11694(11)C13ndashC14ndashC9 12149(11)C13ndashC14ndashN3 13163(11)N3ndashC14ndashC9 10688(10)N3ndashC15ndashC16 11265(10)C17ndashC16ndashC15 12492(15)O1ndashN1ndashC1 11832(10)O2ndashN1ndashC1 11849(11)O2ndashN1ndashO1 12318(11)C8ndashN2ndashC7 12376(10)C8ndashN2ndashC9 10993(10)C9ndashN2ndashC7 12631(10)C8ndashN3ndashC14 11002(10)C8ndashN3ndashC15 12380(10)C14ndashN3ndashC15 12618(10)

stable than the nitrobenzenendashnitrobenzene 120587ndash120587 interactionThe energy difference between the dimmers 1 and 3 is249 kcalmol although it must be taken into considerationthat in the case of the first dimer a second edge to faceinteraction between the benzimidazole and the nitrobenzenefragments is also present The difference in calculated energybetween 2 and 3 is 193 kcalmol

The HOMO and LUMO minus 2 are located on the 1H-benzo[d]imidazol-2(3H)-one moiety and the LUMO andHOMO + 2 on the nitrobenzene ring and therefore theinteraction between these frontier orbitals is the responsibleof the observed 120587ndash120587 interactions Figure 11

Tables 2 3 and 4 summarize all bond lengths bondangles and torsion angles obtained for the X-ray crystalstructure of 5

Table 4 Torsion angles for 5

Dihedral (∘)C1ndashC2ndashC3ndashC4 102(18)C2ndashC1ndashC6ndashC5 minus042(17)C2ndashC1ndashN1ndashO1 1916(16)C2ndashC1ndashN1ndashO2 minus16230(12)C2ndashC3ndashC4ndashC5 minus022(18)C2ndashC3ndashC4ndashC7 minus17868(11)C3ndashC4ndashC5ndashC6 minus094(17)C3ndashC4ndashC7ndashN2 10896(13)C4ndashC5ndashC6ndashC1 124(17)C4ndashC7ndashN2ndashC8 10683(12)C4ndashC7ndashN2ndashC9 minus7363(14)C5ndashC4ndashC7ndashN2 minus6949(14)C6ndashC1ndashC2ndashC3 minus070(18)C6ndashC1ndashN1ndashO1 minus15922(12)C6ndashC1ndashN1ndashO2 1932(17)C7ndashC4ndashC5ndashC6 17754(11)C9ndashC10ndashC11ndashC12 minus059(17)C9ndashC14ndashN3ndashC8 minus049(12)C9ndashC14ndashN3ndashC15 minus17971(10)C10ndashC9ndashC14ndashC13 087(16)C10ndashC9ndashC14ndashN3 minus17918(10)C10ndashC9ndashN2ndashC7 minus025(19)C10ndashC9ndashN2ndashC8 17934(11)C10ndashC11ndashC12ndashC13 057(18)C11ndashC12ndashC13ndashC14 017(17)C12ndashC13ndashC14ndashC9 minus087(16)C12ndashC13ndashC14ndashN3 17920(11)C13ndashC14ndashN3ndashC8 17944(11)C13ndashC14ndashN3ndashC15 023(18)C14ndashC9ndashC10ndashC11 minus012(16)C14ndashC9ndashN2ndashC7 minus17980(10)C14ndashC9ndashN2ndashC8 minus021(12)C16ndashC15ndashN3ndashC8 11184(13)C16ndashC15ndashN3ndashC14 minus6905(15)N1ndashC1ndashC2ndashC3 minus17902(10)N1ndashC1ndashC6ndashC5 17789(10)N2ndashC8ndashN3ndashC14 037(12)N2ndashC8ndashN3ndashC15 17960(10)N2ndashC9ndashC10ndashC11 minus17961(11)N2ndashC9ndashC14ndashC13 minus17952(10)N2ndashC9ndashC14ndashN3 042(11)N3ndashC8ndashN2ndashC7 17951(10)N3ndashC8ndashN2ndashC9 minus009(12)N3ndashC15ndashC16ndashC17 12776(15)O3ndashC8ndashN2ndashC7 minus037(19)O3ndashC8ndashN2ndashC9 minus17998(11)O3ndashC8ndashN3ndashC14 minus17975(11)O3ndashC8ndashN3ndashC15 minus051(19)

4 Conclusions

A new substituted benzo[d]imidazole-2(3H)-one has beensynthesized (1-(4-nitrobenzyl)-3-allyl-1H-benzo[d]imidazol-2(3H)-one) and its crystal structure has been determinedshowing a solid state geometry stabilized by intermolec-ular 120587ndash120587 interactions benzimidazolendashbenzimidazole andnitrobenzenendashnitrobenzene providing the formation of a sta-ble three-dimensional network Computational calculations


have allowed a better understanding of the nature of thoseintermolecular interactions present in the crystal structure

Acknowledgments

Financial support has been provided by GV (PROME-TEO2012020) and MINECO (CTQ2012-38543-C03-01)

References

[1] PW Erhardt ldquoIn search of the digitalis replacementrdquo Journal ofMedicinal Chemistry vol 30 no 2 pp 231ndash237 1987

[2] G L Gravalt B C Baguley W R Wilson and W A DennyldquoDNA-directed alkylating agents 6 Synthesis and antitumoractivity of DNAminor groove-targeted anilinemustard analogsof pibenzimol (Hoechst 33258)rdquo Journal of Medical Chemistryvol 37 pp 4338ndash4345 1994

[3] K-J Soderlind B Gorodetsky A K Singh N R Bachur G GMiller and J W Lown ldquoBis-benzimidazole anticancer agentstargeting human tumour helicasesrdquo Anti-Cancer Drug Designvol 14 no 1 pp 19ndash25 1999

[4] J S Kim B Gatto C Yu A Liu L F Liu and E J LaVoie ldquoSub-stituted 251015840-Bi-1H-benzimidazoles topoisoraerase I inhibitionand cytotoxicityrdquo Journal of Medicinal Chemistry vol 39 no 4pp 992ndash998 1996

[5] T Roth M L Morningstar P L Boyer S H Hughes RW Buckheit Jr and C J Michejda ldquoSynthesis and biologicalactivity of novel nonnucleoside inhibitors of HIV-1 reversetranscriptase 2-Aryl-substituted benzimidazolesrdquo Journal ofMedicinal Chemistry vol 40 no 26 pp 4199ndash4207 1997

[6] Y Bai J Lu Z Shi and B Yang ldquoSynthesis of 215-hexadecanedione as a precursor ofmusconerdquo Synlett vol 12 no4 pp 544ndash546 2001

[7] E Hasegawa A Yoneoka K Suzuki T Kato T Kitazume andK Yanagi ldquoReductive transformation of 120572120573-epoxy ketones andother compounds promoted through photoinduced electrontransfer processes with 13-dimethyl- 2-phenylbenzimidazoline(DMPBI)rdquo Tetrahedron vol 55 no 45 pp 12957ndash12968 1999

[8] E Bouwman W L Driessen and J Reedjik ldquoModel systemsfor type I copper proteins structures of copper coordinationcompounds with thioether and azole-containing ligandsrdquoCoor-dination Chemistry Reviews vol 104 no 1 pp 143ndash172 1990

[9] M A Pujar T D Bharamgoudar and D N SathyanarayanaldquoCobalt(II) nickel(II) and copper(II) complexes of bidentatebibenzimidazolesrdquoTransitionMetal Chemistry vol 13 no 6 pp423ndash425 1988

[10] G-D Zhu V B Gandhi J Gong et al ldquoSynthesis andSAR of novel potent and orally bioavailable benzimidazoleinhibitors of poly(ADP-ribose) polymerase (PARP) with a qua-ternary methylene-amino substituentrdquo Bioorganic and Medici-nal Chemistry Letters vol 18 no 14 pp 3955ndash3958 2008

[11] Y Ogino N Ohtake Y Nagae et al ldquoDesign syntheses andstructure-activity relationships of novel NPY Y5 receptorantagonists 2-3-Oxospiro[isobenzofuran-1(3H)41015840-piperidin]-11015840-ylbenzimidazole derivativesrdquo Bioorganic and MedicinalChemistry Letters vol 18 no 18 pp 5010ndash5014 2008

[12] D I Shah M Sharma Y Bansal G Bansal and M SinghldquoAngiotensin II-AT

1receptor antagonists design synthesis and

evaluation of substituted carboxamido benzimidazole deriva-tivesrdquo European Journal of Medicinal Chemistry vol 43 no 9pp 1808ndash1812 2008

[13] D Belaziz Y Kandri Rodi F Ouazzani Chahdi E Essassi MSaadi and L E Ammari ldquo1-Allyl-1H-13-benzimidazol-2(3H)-onerdquo Acta Crystallographica vol E68 article o3212 2012

[14] D Belaziz Y Kandri Rodi A Kandri Rodi E MEssassi M Saadi and L E Ammari ldquoEthyl 2-oxo-3-(3-phthalimidopropyl)-2 3-dihydro-1H-1 3-benzimidazole-1-carboxylaterdquo Acta Crystallographica vol E69 pp o641ndasho6422013

[15] Y Kandri Rodi F Ouazzani Chahdi E M Essassi S V LuisM Bolte and L El Ammari ldquo13-Dibenzyl-1H-benzimidazol-2(3H)-onerdquoActaCrystallographica vol 67 no 12 p o3234 2011

[16] O VDolomanov L J Bourhis R J Gildea J A KHoward andH Puschmann ldquoOLEX2 a complete structure solution refine-ment and analysis programrdquo Journal of Applied Crystallographyvol 42 no 2 pp 339ndash341 2009

[17] G M Sheldrick ldquoa short history of SHELXrdquo Acta Crystallo-graphica vol A64 pp 112ndash122 2008

[18] C FMacrae I J Bruno J A Chisholm et al ldquoMercuryCSD20new features for the visualization and investigation of crystalstructuresrdquo Journal of Applied Crystallography vol 41 no 2 pp466ndash470 2008

[19] L L C Schrodinger The PyMOL Molecular Graphics SystemVersion 13

[20] B J Deppmeier A J Driessen T S Hehre et al Spartan rsquo08build 132 Wavefunction Irvine Calif USA 2009

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Volume 2013

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Journal of

Spectroscopy


C11

C9C13

C10

C12

C14

N3N2

C8

O3

C17C16 C15

C4

C7

C3

C5 C6

O1C2

N1

O2

C1

Figure 1 ORTEP representation of 5 (displacement ellipsoids are drawn at the 50 probability level)

Figure 2 The unique molecule in the crystal structure of 5 (displacement ellipsoids are drawn at the 50 probability level)

(5)

N

N

O

NO2

Scheme 1

To the formerly obtained compound (3) (017 g 063mmol) allylbromide (4) (009 g 076mmol) in DMF (10mL)potassium carbonate (010 g 076mmol) and tetra-n-buty-lammonium bromide (002 g 0063mmol) were added(Scheme 3) Stirring was continued at room temperature for12 hours The salt was removed by filtration and the filtrateconcentrated under reduced pressure The residue was sep-arated by chromatography on a silica gel column with ethylacetatehexane (1 1) as the eluent The obtained compound(5) was recrystallized from dichloromethanehexane to givecolorless crystals of 5 (melting point = 95∘C yield = 87)

Single crystals of 5 were obtained from dichlorometh-anehexane to give colorless crystals A suitable crystalwas selected and measured on an Agilent SuperNova Atlas

Dual Source Agilent Technologies diffractometer using theCrysAlisPro softwareThe crystal was kept at 20000K duringdata collection Using Olex2 [16] the structure was solvedwith the ShelXS [17] structure solution program using directmethods and refined with the ShelXL [17] refinement pack-age using least squares minimization All hydrogen atomswere fixed in geometrical positions Nonhydrogen atomswere refined with anisotropic displacement parameters Themolecular connectivity and the crystal packing diagramweredrawn using the Mercury (CCDC) program [18] and PyMol[19] Geometrical measurements were carried out using theMercury (CCDC) program [18]

Crystal Data for 5 C17H15N3O3(M = 30932) mon-

oclinic space group P21n (no 14) a = 712148(8) A b

= 1612035(17) A c = 1304169(17) A 120573 = 933043(11) V= 149471(3) A3 Z = 4 T = 20000(10) K 120583(Cu K120572) =0795mmminus1119863calc = 1375 gmm3 14200 reflections measured(874 le 2Θ le 14606) 2935 unique (119877int = 00215) which wereused in all calculationsThe final 119877

1was 00353 (gt2sigma(I))

and wR2was 00962 (all data) CCDC number 948080 See

Figure 1 for the ORTEP representation of 5In order to obtain an additional insight into the inter-

molecular forces determining the crystal packing compu-tational calculations were used for the optimization of themolecule and the calculation of the energies associated tothe different intermolecular interactions at the PM3 level ofcalculation using the Spartanrsquo08 software [20]


NH

NHO

NH

NO

BTBADMFrt

Br

(1) (2) (3)7012eq

K2CO3

NO2

NO2

+

Scheme 2

NH

NO

Br N

NO+

BTBADMFrt

12eq 87(3) (4) (5)

K2CO3

NO2NO2

Scheme 3











1= 00353 119908119877

2= 00930


2= 00962




36103005

3703


3610

3703

3610


3733



ao

c

b














NN NN O2N


O2N

NO2NO2

O2N

NO2

NO

O

O

O

NO

NNNN O

NN

360 361 362 369 370 371 372 373 374 375

4135

4140

4145

4150

4155

4160

4165

PM3

ener

gy (k

calm

ol)




HOMO












4 Conclusions




Acknowledgments


References
































ISRN Chromatography






CatalystsJournal of






Advances in

Physical Chemistry








Journal of

Chemistry







Journal of

Volume 2013




Journal of

Spectroscopy


NH

NHO

NH

NO

BTBADMFrt

Br

(1) (2) (3)7012eq

K2CO3

NO2

NO2

+

Scheme 2

NH

NO

Br N

NO+

BTBADMFrt

12eq 87(3) (4) (5)

K2CO3

NO2NO2

Scheme 3











1= 00353 119908119877

2= 00930


2= 00962




36103005

3703


3610

3703

3610


3733



ao

c

b














NN NN O2N


O2N

NO2NO2

O2N

NO2

NO

O

O

O

NO

NNNN O

NN

360 361 362 369 370 371 372 373 374 375

4135

4140

4145

4150

4155

4160

4165

PM3

ener

gy (k

calm

ol)




HOMO












4 Conclusions




Acknowledgments


References
































ISRN Chromatography






CatalystsJournal of






Advances in

Physical Chemistry








Journal of

Chemistry







Journal of

Volume 2013




Journal of

Spectroscopy


36103005

3703


3610

3703

3610


3733



ao

c

b














NN NN O2N


O2N

NO2NO2

O2N

NO2

NO

O

O

O

NO

NNNN O

NN

360 361 362 369 370 371 372 373 374 375

4135

4140

4145

4150

4155

4160

4165

PM3

ener

gy (k

calm

ol)




HOMO












4 Conclusions




Acknowledgments


References
































ISRN Chromatography






CatalystsJournal of






Advances in

Physical Chemistry








Journal of

Chemistry







Journal of

Volume 2013




Journal of

Spectroscopy











NN NN O2N


O2N

NO2NO2

O2N

NO2

NO

O

O

O

NO

NNNN O

NN

360 361 362 369 370 371 372 373 374 375

4135

4140

4145

4150

4155

4160

4165

PM3

ener

gy (k

calm

ol)




HOMO












4 Conclusions




Acknowledgments


References
































ISRN Chromatography






CatalystsJournal of






Advances in

Physical Chemistry








Journal of

Chemistry







Journal of

Volume 2013




Journal of

Spectroscopy









4 Conclusions




Acknowledgments


References
































ISRN Chromatography






CatalystsJournal of






Advances in

Physical Chemistry








Journal of

Chemistry







Journal of

Volume 2013




Journal of

Spectroscopy



Acknowledgments


References
































ISRN Chromatography






CatalystsJournal of






Advances in

Physical Chemistry








Journal of

Chemistry







Journal of

Volume 2013




Journal of

Spectroscopy










ISRN Chromatography






CatalystsJournal of






Advances in

Physical Chemistry








Journal of

Chemistry







Journal of

Volume 2013




Journal of

Spectroscopy

synthesis and crystal structure of 1-(4-nitrobenzyl)-3...

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