Meta-Siyanobenzil-Sübstitüentli NHC İçeren Yeni Pd(II)PPh3 Kompleksi: Kristal Yapı ve Hesaplamalı Çalışmalar

Year 2022, Volume: 12 Issue: 4, 2188 - 2198, 01.12.2022

Betül Şen

https://doi.org/10.21597/jist.1160050

Abstract

Meta-siyanobenzil sübstitüentli NHC ve trifenilfosfin içeren paladyum(II) bileşiğinin kristal yapısı, tek kristal XRD yöntemi ile belirlendi. Moleküler geometrinin optimize hali, GEN baz seti kullanılarak DFT/B3LYP hibrit fonksiyonel yöntemi yardımıyla araştırılmıştır. Enerji aralığını hesaplamak ve yumuşaklık, sertlik, kimyasal potansiyel ve elektronegatiflik gibi bazı moleküler özellikleri belirlemek için HOMO ve LUMO analizleri kullanıldı. Ayrıca, hiperkonjugatif etkileşimlerden kaynaklanan molekül stabilitesi ve yük delokalizasyonu, doğal bağ orbital analizinden yararlanılarak gerçekleştirilmiştir. DFT yöntemi ile atomik yük analizi de yapılmıştır.

Keywords

N-heterosiklik karbenler, kristal yapı, DFT

New Pd(II)PPh3 Complex Bearing Meta-Cyanobenzyl-Substituted NHC: Crystal Structure and Computational Studies

Abstract

Crystal structure of palladium(II) complex containing meta-cyanobenzyl substituted NHC and triphenylphosphine were established by single-crystal XRD method. The molecular geometry in optimized form has been studied based on DFT/B3LYP hybrid functional method using the GEN basis set. The HOMO and LUMO analyses are used to compute the energy gap and to determine a number of molecular properties including softness, hardness, chemical potential, and electronegativity. Besides, the molecular stability due to hyperconjugative interactions and charge delocalization have been executed benefiting from the natural bond orbital analysis. Also, atomic charge analysis was conducted by the DFT method.

Keywords

N-heterocyclic carbenes, crystal structure, DFT

References

• Abbas A, Gökce H, Bahceli S, Bolte M, Naseer MM, 2016. Solid state structural and theoretical investigations of a biologically active chalcone. Journal of Molecular Structure, 1112: 124–135.
• Akkoç S, Kayser V, Özer I, Hibbs DE, Gök Y, Williams PA, Hawkins B, Lai F, 2017. New Compounds Based on a Benzimidazole Nucleus: Synthesis, Characterization and Cytotoxic Activity Against Breast and Colon Cancer Cell Lines. Journal of Organometallic Chemistry, 839: 98-107.
• Aktaş A, Barut Celepci D, Gök Y, Aygün M, 2018. 2-Hydroxyethyl-Substituted Pd-PEPPSI Complexes: Synthesis, Characterization and the Catalytic Activity in the Suzuki-Miyaura Reaction for Aryl Chlorides in Aqueous Media. ChemistrySelect, 3: 9974–9980.
• Aktaş A, Celepci DB, Gök Y, Aygün M, 2018. 2-Hydroxyethyl-Substituted (NHC)Pd(II)PPh3 Complexes: Synthesis, Characterization, Crystal Structure and Its Application on Sonogashira Cross-Coupling Reactions in Aqueous Media. ChemistrySelect, 3(39): 10932–10937.
• Aktaş A, Erdemir F, Barut Celepci D, Gök Y, Aygün M, 2019. Mixed phosphine/N-heterocyclic carbene–palladium complexes: synthesis, characterization, crystal structure and application in the Sonogashira reaction in aqueous media. Transition Metal Chemistry, 44: 229-236.
• Aravinda RP, Babul RA, Ramachandra RG, Subbarami RN, 2013. Suzuki–Miyaura Cross‐Coupling Reaction of Naphthyl Triflate with Indole Boronic Acids Catalyzed by a Recyclable Polymer‐Supported N‐Heterocyclic Carbene–Palladium Complex Catalyst: Synthesis of Naphthalene‐Linked Bis‐ Heterocycles. Journal of Heterocyclic Chemistry, 50(6): 1451-1456.
• Arduengo AJ, Harlow RL, Kline M, 1991. A stable crystalline carbene. Journal of the American Chemical Society, 113(1): 361–363.
• Asma M, Badshah A, Ali S, Sohail M, Fettouhi M, Ahmad S, Malik A, 2006. Synthesis, characterization of mixed ligand palladium (II) complexes of triphenylphosphine and anilines and their enzyme inhibition studies against βglucuronidase. The crystal structure of trans-dichloro-(mchloroaniline) (triphenylphosphine) palladium (II). Transition Metal Chemistry, 31: 556- 559.
• Bal S, Demirci Ö, Şen B, Taslimi P, Aktaş A, Gök Y, Aygün M, Gülçin İ, 2021. PEPPSI type Pd(II)NHC complexes bearing chloro-/fluorobenzyl group: Synthesis, characterization, crystal structures, α- glycosidase and acetylcholinesterase inhibitory properties. Polyhedron, 198: 115060.
• Becke AD, 1993. Density‐functional thermochemistry. III. The role of exact exchange. The Journal of Chemical Physics, 98: 5648. Benhamou L, Besnard C, Kündig EP, 2014. Chiral PEPPSI Complexes: Synthesis, Characterization, and Application in Asymmetric Suzuki–Miyaura Coupling Reactions. Organometallics, 33: 260-266.
• Bernstein J, Davis RE, Shimoni L, Chang NL, 1995. Patterns in Hydrogen Bonding: Functionality and Graph Set Analysis in Crystals. Angewandte Chemie International Edition in English, 34(15): 1555-1573.
• Bhojane JM, Jadhav VG, Nagarkar JM, 2017. Pd(NHC)PEPPSI-diazonium salts: an efficient blend for the decarboxylative Sonogashira cross coupling reaction. New Journal of Chemistry, 41(14): 6775-6780.
• Bondi A, 1964. van der Waals Volumes and Radii. The Journal of Physical Chemistry, 68(3): 441-451.
• Boubakri L, Yasar S, Dorcet V, Roisnel T, Bruneau C, Hamdi N, Ozdemir I, 2017. Synthesis and catalytic applications of palladium N-heterocyclic carbene complexes as efficient pre-catalysts for Suzuki–Miyaura and Sonogashira coupling reactions. New Journal of Chemistry, 41(12): 5105-5113.
• Caló V, Sole RD, Nacci A, Schingaro E, Scordari F, 2000. Synthesis and Crystal Structure of Bis(2,3-dihydro-3-methylbenzothiazole-2-ylidene)palladium(II) Diiodide: The First Palladium Complex with Benzothiazole Carbene Ligands Suitable for Homogeneous Catalysis. European Journal of Organic Chemistry, 869–871.
• Cavallo L, Correa A, Costabile C, Jacobsen H, 2005. Steric and electronic effects in the bonding of N-heterocyclic ligands to transition metals. Journal of the Organometallic Chemistry, 690: 5407-5413.
• Cinderella AP, Vulovic B, Watson DA, 2017. Palladium-Catalyzed Cross-Coupling of Silyl Electrophiles with Alkylzinc Halides: A Silyl-Negishi Reaction. Journal of the American Chemical Society, 139(23): 7741-7744.
• CrysAlisPro Software System, Rigaku Corporation, Oxford, UK, 2015. Version 1.171.38.43.
• Dahm G, Bailly C, Karmazin L, Bellemin-Laponnaz S, 2015. Synthesis, structural characterization and in vitro anti-cancer activity of functionalized N-heterocyclic carbene platinum and palladium complexes. Journal of Organometallic Chemistry, 794: 115–124. Dehimat ZI, Yaşar S, Tebbani D, Özdemir İ, 2018. Sonogashira cross-coupling reaction catalyzed by N-heterocyclic carbene-Pd(II)-PPh3 complexes under copper free and aerobic conditions. Inorganica Chimica Acta, 469: 325-334.
• Dennington R, Keith TA, Millam JM, 2016. GaussView, Version 6, Semichem Inc. Shawnee Mission. KS.
• Dolomanov OV, Bourhis LJ, Gildea RJ, Howard JAK, Puschmann H, 2009. OLEX2: A complete structure solution, refinement and analysis program. Journal. Applied Crystallography, 42: 339-341.
• Dragutan V, Dragutan I, Delaude L, Demonceau A, 2007. NHC-Ru complexes-Friendly catalytic tools for manifold chemical transformations. Coordination Chemistry Reviews, 251(5-6): 765-794.
• Erdemir F, Barut Celepci D, Aktaş A, Gök Y, 2019. 2-hydroxyethyl-substituted (NHC)PdI2 (pyridine) (Pd-PEPPSI) complexes: synthesis, characterization and the catalytic activity in the sonogashira cross-coupling reaction. ChemistrySelect, 4: 5585-5590.
• Erdoğan H, Aktaş A, Gök Y, Sarı Y 2018. N-Propylphthalimide-substituted bis-(NHC)PdX2 complexes: synthesis, characterization and catalytic activity in direct arylation reactions. Transition Metal Chemistry, 43: 31-37.
• Foster JP, Weinhold F, 1980. Natural hybrid orbitals. Journal of the American Chemical Society, 102(24): 7211-7218.
• Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, Barone V, Petersson, GA, Nakatsuji H, Li X, Caricato M, Marenich A, Bloino J, Janesko B G, Gomperts R, Mennucci B, Hratchian HP, Ortiz JV, Izmaylov AF, Sonnenberg JL, Williams-Young D, Ding F, Lipparini F, Egidi F, Goings J, Peng B, Petrone A, Henderson T, et al., 2010. Gaussian 09 Revision B.01. Gaussian, Inc. Wallingford CT.
• Glendening ED, Landis CR, Weinhold F, 2013. Nbo 6.0: Natural bond orbital analysis program. Journal of Computational Chemistry, 34: 1429-1437.
• Glendening E D, Badenhoop JK, Reed AE, Carpenter JE, Bohmann JA, Morales CM, Landis CR, Weinhold F, 2013. NBO 6.0. Theoretical Chemistry Institute, University of Wisconsin, Madison, WI, http://nbo6.chem.wisc.edu/
• Gorelsky SI, Ghosh S, Solomon EI, 2006. Mechanism of N2O Reduction by the μ4-S Tetranuclear CuZ Cluster of Nitrous Oxide Reductase. Journal of the American Chemical Society, 128(1): 278–290.
• Gök Y, Aktas A, Erdoğan H, Sarı Y, 2018. New 4-vinylbenzyl-substituted bis(NHC)-Pd(II) complexes: Synthesis, characterization and the catalytic activity in the direct arylation reaction. Inorganica Chimica Acta, 471: 735-740.
• Gökçe AG, Gülcemal S, Aygün M, Çetinkaya B, Büyükgüngör O, 2006. trans-Bis[1-benzyl-3-(2,3,4,5,6-pentafluorobenzyl)benzimidazol-2-ylidene]dibromopalladium(II). Acta Crystallographica Section C Crystal Structure Communications. 62(11): m535–m537.
• Guram AS, Buchwald SL, 1994. Palladium-Catalyzed Aromatic Aminations with in situ Generated Aminostannanes. Journal of the Americal Chemical Society, 116:7901-7902.
• Herrmann WA, Öfele K, Preysing D, Schneider SK, 2003. Phospha-palladacycles and N-heterocyclic carbene palladium complexes: efficient catalysts for CC-coupling reactions. Journal of Organometallic Chemistry, 687(2): 229–248.
• Hu X, Castro-Rodriguez I, Olsen K, Meyer K, 2004. Group 11 Metal Complexes of N-Heterocyclic Carbene Ligands: Nature of the Metal-Carbene Bond. Organometallics, 23: 755-764.
• Huynh HV, Ho JH, Neo TC, Koh LL, 2005. Solvent-controlled selective synthesis of a trans-configured benzimidazoline-2-ylidene palladium(II) complex and investigations of its Heck-type catalytic activity. Journal of Organometallic Chemistry, 690: 3854–3860.
• Jafarpour L, Nolan SP, 2000. Transition-metal systems bearing a nucleophilic carbene ancillary ligand: from thermochemistry to catalysis. Advances in Organometallic Chemistry, 46: 181-222.
• Janiak C, 2000. A critical account on π-π stacking in metal complexes with aromatic nitrogen-containing ligands. Journal of the Chemical Society, Dalton Transactions, 21: 3885–3896.
• Lee C, Yang W, Parr RG, 1988. Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Physical Review, 37: 785.
• Liao CY, Chan KT, Tu CY, Chang YW, Hu CH, Lee HM, 2009. Robust and electron-rich cis-palladium(II) complexes with phosphine and carbene ligands as catalytic precursors in Suzuki coupling reactions. Chemistry-A European Journal, 15: 405-417.
• Lin YC, Hsueh HH, Kanne S, Chang LK, Liu FC, Lin IJB, Lee GH, Peng SM, 2013. Efficient PEPPSI-Themed Palladium N-Heterocyclic Carbene Precatalysts for the Mizoroki–Heck Reaction. Organometallics, 32: 3859-3869.
• Palafox MA, 2018. DFT computations on vibrational spectra: Scaling procedures to improve the wavenumbers. Physical Sciences Reviews, 3: 1-30.
• Osińska M, Gniewek A, Trzeciak AM, 2016. Suzuki–Miyaura and Hiyama coupling catalyzed by PEPPSI-type complexes with non-bulky NHC ligand. Journal of Molecular Catalysis A: Chemical, 418-419: 9-18.
• Öfele K, 1968. 1,3-Dimethyl-4-imidazolinyliden-(2)-pentacarbonylchrom ein neuer übergangsmetall-carben-komplex. Journal of Organometallic Chemistry, 12(3): 42-43.
• Özdemir İ, Arslan H, Demir S, VanDerveer D, Çetinkaya B, 2011. Synthesis, characterization and catalytic properties of cis-dibromo{1,1′-di[3,4,5-trimethoxybenzyl]-3,3′-butylenedibenzi midazol-2,2′-diylidene}palladium (II). Inorganic Chemistry Communications, 14(5): 672–675.
• Sarı Y, Aktaş A, Barut Celepci D, Gök Y, Aygün M, 2017. Synthesis, Characterization and Crystal Structure of New 2-Morpholinoethyl-Substituted Bis-(NHC)Pd(II) Complexes and the Catalytic Activity in the Direct Arylation Reaction. Catalysis Letters, 147: 2340-2351.
• Sheldrick GM, 2015. SHELXT-integrated space-group and crystal-structure determination. Acta Crystallographica A Foundations and Advances, A71: 3-8.
• Sheldrick GM, 2015. Crystal structure refinement with SHELXL. Acta Crystallographica C Structural Chemistry, C71: 3-8.
• Spek AL, 2003. Single-crystal structure validation with the program PLATON. Journal of Applied Crystallography, 36: 7-13.
• Spek AL, 2009. Structure validation in chemical crystallography. Acta Crystallographica D65, 148-155.
• Valentine Jr DH, Hillhouse JH, 2003. Electron-Rich Phosphines in Organic Synthesis II. Catalytic Applications. Synthesis, 16: 2437-2460.
• Velazquez HD, Verpoort F, 2012. N-heterocyclic carbene transition metal complexes for catalysis in aqueous media. Chemical Society Reviews, 41(21), 7032-7060.
• Wanzlick HW, Schönherr HJ, 1968. Direct Synthesis of a Mercury Salt-Carbene Complex. Angewandte Chemie International Edition in English, 7(2): 141-142.
• Weinhold F, Landis CR, Glendening ED, 2016. What is NBO analysis and how is it useful? International Reviews in Physical Chemistry, 35(3): 399–440.
• Zhong R, Lindhorst AC, Groche FJ, Kühn FE, 2017. Immobilization of N-Heterocyclic Carbene Compounds: A Synthetic Perspective. Chemical Reviews, 117(3): 1970–2058.