VIBRATIONAL SPECTROSCOPIC STUDY OF PYRIDINE AND PYRIMIDINE LIGANDS COORDINATED WITH ANTIMONY (III) COMPLEXES: INSIGHTS FROM DFT CALCULATIONS

Yıl 2023, , 125 - 142, 28.08.2023

Berna Çatıkkaş , Özge Şahinler

https://doi.org/10.20290/estubtdb.1282541

Öz

By employing the Scaled Quantum Mechanics Force Field (SQMFF) methodology, a comprehensive analysis was conducted to assign the vibrational spectra of three antimony (III) compounds, [1a-3a], that possess pyridine and pyrimidine ligands. The potential energy distribution (PED) was calculated and utilized to assign the IR spectra of the antimony (III) compounds. The theoretical frontier molecular orbital descriptors, the partial and total density of state distribution (TDOS, PDOS), molecular electronic potential surface map (MEP), nonlinear optical properties (NLO) of these complexes also were computed and investigated. The DFT/B3LYP/GEN (C, H, N, Cl: 6-31G(d,p) and Sb: LanL2DZ) level was utilized for all DFT calculations using the Gaussian 09W program. Furthermore, theoretical frontier molecular orbital descriptors, including electronegativity, chemical potential, softness, electrophilicity index, and electron affinity for six antimony (III) compounds were calculated ([1a/1b-3a/3b]). The results showed that, the ionization potential energy value of the [3a], which had the lowest experimental Leishmania activity, was also found to be the lowest among the others.

Anahtar Kelimeler

Antimony (III) compounds, Scaled Quantum Mechanical Force Field, Nonlinear Optics, Infrared Spectra, Density Functional Theory

Destekleyen Kurum

The Research Foundation of Hatay Mustafa Kemal University

Proje Numarası

16860

Teşekkür

This study was supported by the Research Foundation of Hatay Mustafa Kemal University Project No: 16860. I would like to thanks the Gazi University for providing Gaussian 09W Software. The numerical calculations reported in this paper were performed at TUBITAK ULAKBIM, High Performance and Grid Computing Center (TRUBA Resources).

VIBRATIONAL SPECTROSCOPIC STUDY OF PYRIDINE AND PYRIMIDINE LIGANDS COORDINATED WITH ANTIMONY (III) COMPLEXES: INSIGHTS FROM DFT CALCULATIONS

Öz

Ölçeklendirilmiş Kuantum Mekaniği Kuvvet Alanı (SQMFF) metodolojisi kullanılarak, piridin ve pirimidin ligandlarına sahip üç antimon (III) bileşiğinin [1a-3a], titreşim spektrumlarını işaretlemek için kapsamlı bir analiz yapılmıştır. Antimon (III) bileşiklerinin IR spektrumlarını işaretlemek için Potansiyel enerji dağılımı (PED) hesaplandı ve kullanıldı. Teorik olarak moleküler orbital diskriptörleri, kısmi ve toplam durum yoğunluğu dağılımı (TDOS, PDOS), moleküler elektronik potansiyel yüzey haritası (MEP), doğrusal olmayan optik özellikleri (NLO) de hesaplanmış ve incelenmiştir. Gaussian 09W programı kullanılarak yapılan tüm DFT hesaplamaları için DFT/B3LYP/LanL2DZ metot ve gen seti kullanılmıştır. Ayrıca, altı antimon (III) bileşiği için elektronegatiflik, kimyasal potansiyel, yumuşaklık, elektrofiliklik indeksi ve elektron ilgisi olmak üzere teorik sınır moleküler orbital diskriptörleri hesaplanmıştır ([1a/1b-3a/3b]). Elde edilen sonuçlar, en düşük deneysel Leishmania aktivitesine sahip olan [3a] bileşiğinin iyonizasyon potansiyel enerjisinin, diğer bileşikler arasında en düşük değere sahip olduğunu göstermektedir.

Anahtar Kelimeler

Antimony (III) compounds, Scaled Quantum Mechanical Force Field, Nonlinear Optics, Infrared Spectra, Density Functional Theory

Proje Numarası

16860

Kaynakça

• [1] Beyersmann D, Hartwig A. Carcinogenic metal compounds: recent insight into molecular and cellular mechanisms 2008; 82: 493–512.
• [2] Krebs RE. The history and use of our earth’s chemical elements: a reference guide. Greenwood Publishing Group 2006.
• [3] Ulrich N. Antimony 2003; 81: 126.
• [4] Estes JW. The medical skills of ancient Egypt. Science History Publications/USA 1993.
• [5] Duffin J, René P. “Anti–moine; Anti–biotique”: The Public Fortunes of the Secret Properties of Antimony Potassium Tartrate (Tartar Emetic) 1991; 46: 440–56.
• [6] Herwaldt BL. Vol. 354 1999: 1191–99.
• [7] Gielen M, Tiekink ERT. Metallotherapeutic drugs and metal-based diagnostic agents: the use of metals in medicine. John Wiley & Sons 2005.
• [8] Mjos KD, Orvig C. Metallodrugs in Medicinal Inorganic Chemistry 2014; 114: 4540–63.
• [9] Burford N, Carpenter Y, Conrad E, Saunders CDL. The Chemistry of Arsenic, Antimony and Bismuth. In: Hongzhe Sun, Ed. Biol. Chem. Arsenic, Antimony Bismuth.; John Wiley & Sons Ltd. 2011; pp. 1–18.
• [10] Murray HW, Berman JD, Davies CR, Saravia NG. Advances in leishmaniasis 2005; 366: 1561–77.
• [11] Newlove T, Guimarães LH, Morgan DJ, Alcântara L, Glesby MJ, Carvalho EM, et al. Antihelminthic therapy and antimony in cutaneous leishmaniasis: A randomized, double-blind, placebo-controlled trial in patients co-infected with helminths and leishmania braziliensis 2011; 84: 551–55.
• [12] Baiocco P, Colotti G, Franceschini S, Ilari A. Molecular basis of antimony treatment in Leishmaniasis 2009; 52: 2603–12.
• [13] Magill AJ, Strickland GT, Maguire JH, Ryan ET, Solomon T. Hunter’s tropical medicine and emerging infectious disease. Elsevier Health Sciences 2012.
• [14] Dostál L, Jambor R, Růžička A, Jirásko R, Černošková E, Beneš L, et al. [2 + 2] Cycloaddition of Carbon Disulfide to NCN-Chelated † Organoantimony(III) and Organobismuth(III) Sulfides: Evidence for Terminal Sb−S and Bi−S Bonds in Solution ‡ 2010; 29: 4486–90.
• [15] Matsukawa S, Yamamichi H, Yamamoto Y, Ando K. Pentacoordinate Organoantimony Compounds That Isomerize by Turnstile Rotation 2009; 131: 3418–19.
• [16] Moiseev DV, Morugova VA, Gushchin AV., Shavirin AS, Kursky YA, Dodonov VA. Tetraphenylantimony carboxylates in the cascade Pd-catalyzed C-phenylation reaction of methyl acrylate in the presence of peroxide 2004; 689: 731–37.
• [17] Abboud KA, Palenik RC, Palenik GJ, Wood RM. Syntheses and structures of four antimony complexes with planar tridentate pyridine ligands 2007; 360: 3642–46.
• [18] Prokudina Y V, Davydova EI, Virovets A, Stöger B, Peresypkina E, Pomogaeva A V, et al. Structures and Chemical Bonding in Antimony(III) Bromide Complexes with Pyridine 2020; 26: 16338–48.
• [19] Davydova EI, Virovets A, Peresypkina E, Pomogaeva A V, Timoshkin AY. Crystal structures of antimony(III) chloride complexes with pyridine 2019; 158: 97–101.
• [20] Tunҫ T, Koҫ Y, Aҫik L, Karacan MS, Karacan N. DNA cleavage, antimicrobial studies and a DFT-based QSAR study of new antimony(III) complexes as glutathione reductase inhibitor 2015; 136: 1418–27.
• [21] Tunç T, Karacan MS, Ertabaklar H, Sarı M, Karacan N, Büyükgüngör O. Antimony(III) complexes with 2-amino-4,6-dimethoxypyrimidines: Synthesis, characterization and biological evaluation. 2015; 153: 206–14.
• [22] Karacan MS, Rodionova MV., Tunç T, Venedik KB, Mamaş S, Shitov A V., et al. Characterization of nineteen antimony(III) complexes as potent inhibitors of photosystem II, carbonic anhydrase, and glutathione reductase 2016; 130: 167–82.
• [23] Frisch MJ et al. Gaussian 09, Revision A.02 2009.
• [24] O’boyle NM, Tenderholt AL, Langner KM. cclib: A library for package-independent computational chemistry algorithms 2008; 29: 839–45.
• [25] Politzer P, Laurence PR, Jayasuriya K. Molecular electrostatic potentials: An effective tool for the elucidation of biochemical phenomena 1985; VOL. 61: 191–202.
• [26] Politzer P, Murray JS. The fundamental nature and role of the electrostatic potential in atoms and molecules 2002; 108: 134–42.
• [27] Hofacker GL. Peter Politzer und Donald G. Truhlar: Chemical Applications of Atomic and Molecular Electrostatic Potentials, Plenum Press, New York und London 1981. 472 Seiten, Preis: $ 55.- 1982; 86: 872–73.
• [28] Kurtz HA, Stewart JJP, Dieter KM. Calculation of the nonlinear optical properties of molecules 1990; 11: 82–87.
• [29] Fogarasi G, Zhou X, Taylor PW, Pulay P. The calculation of ab initio molecular geometries: efficient optimization by natural internal coordinates and empirical correction by offset forces 1992; 114: 8191–8201.
• [30] Pulay P, Fogarasi G, Pongor G, Boggs JE, Vargha A. Combination of theoretical ab initio and experimental information to obtain reliable harmonic force constants. Scaled quantum mechanical (QM) force fields for glyoxal, acrolein, butadiene, formaldehyde, and ethylene 1983; 105: 7037–47.
• [31] Parallel Quantum Solutions, SQM 2013.
• [32] Parr RG, Szentpály L v, Liu S. Electrophilicity index 1999; 121: 1922–24.
• [33] Koopmans T. Über die Zuordnung von Wellenfunktionen und Eigenwerten zu den Einzelnen Elektronen Eines Atoms 1934; 1: 104–13.
• [34] Tunç T, Ertabaklar H, Karacan N. In vitro anti-leishmanial activities and structure-activity relationship analysis of new antimony(III) complexes 2020; 59: 1609–17.
• [35] Andraud C, Brotin T, Garcia C, Pelle F, Goldner P, Bigot B, et al. Theoretical and experimental investigations of the nonlinear optical properties of vanillin, polyenovanillin, and bisvanillin derivatives 1994; 116: 2094–2102.
• [36] Geskin VM, Lambert C, Brédas J-L. Origin of high second-and third-order nonlinear optical response in ammonio/borato diphenylpolyene zwitterions: the remarkable role of polarized aromatic groups 2003; 125: 15651–58.
• [37] Socrates G. Infrared and Raman characteristic group frequencies. 2004.
• [38] Varsányi G. Vibrational spectra of benzene derivatives. Elsevier 2012.
• [39] Zickgraf A, Bräu E, Dräger M. As(III)/Sb(III)/Bi(III)–halide distances and stretching vibrations. An application of the Varshni relationship upon hypervalent group 15 compounds 1998; 54: 85–90.