Synthesis, Characterization, Spectral Analysis and Molecular Simulation Studies of compounds formed by 2-mercaptopyridine and 1,4-dioxane ligands with some metal(II) chlorides
In particular, the vibration frequencies obtained experimentally of these compounds and the vibration frequencies theoretically calculated with B3LYP/LanL2DZ are substantially compatible with each other.
📌 3 Key Takeaways
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Objective & Hypothesis:In this investigation, two novel coordination compounds in crystalline form were synthesized utilizing chemical substances including 2-mercaptopyridine (2MP), 1,4-dioxane (pD), nickel(II) chloride (NiCl2), and cadmium(II) chloride (CdCl2), followed by an exploration of their structural properties through various experimental techniques.
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Key Findings & Data:In addition, molecular modelling studies were carried out with B3LYP/LanL2DZ level using Gaussian 03 program.
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Conclusion & Impact:In particular, the vibration frequencies obtained experimentally of these compounds and the vibration frequencies theoretically calculated with B3LYP/LanL2DZ are substantially compatible with each other.
In this investigation, two novel coordination compounds in crystalline form were synthesized utilizing chemical substances including 2-mercaptopyridine (2MP), 1,4-dioxane (pD), nickel(II) chloride (NiCl2), and cadmium(II) chloride (CdCl2), followed by an exploration of their structural properties through various experimental techniques. In addition, molecular modelling studies were carried out with B3LYP/LanL2DZ level using Gaussian 03 program. HOMO and LUMO orbitals, NBO studies were obtained by computation. The results from both experimental and optimized structural data were consistent. In particular, the vibration frequencies obtained experimentally of these compounds and the vibration frequencies theoretically calculated with B3LYP/LanL2DZ are substantially compatible with each other.
Kartal, Z., Şahin, Z. S. (2024). Synthesis, Characterization, Spectral Analysis and Molecular Simulation Studies of compounds formed by 2-mercaptopyridine and 1,4-dioxane ligands with some metal(II) chlorides. Gazi University Journal of Science, Volume: 37 Issue: 4. https://doi.org/10.35378/gujs.1359705
Batten, S.R., Champness, N.R., Chen, X.M., Garcia-Martinez, J., Kitagawa, S., Öhrström, L., O’Keeffe, M., Suh, P., Reedijk, J., “Terminology of metal–organic frameworks and coordination polymers (IUPAC Recommendations 2013)”, Pure and Applied Chemistry, 85(8): 1715-1724, (2013). DOI: https://doi.org/10.1351/PAC-REC-12-11-20
Fromm, K., “Coordination polymer networks with s-block metal ions”, Coordination Chemistry Reviews; 252 (8–9): 856-885, (2008). DOI: https://doi.org/10.1016/j.ccr.2007.10.032
Yang, Y., Jiang, G., Li, Y.Z., Bai, J., Pan, Y., You, X.Z., “Synthesis, structures and properties of alkaline earth metal benzene-1.4-dioxylacetates with three-dimensional hybrid networks”, Inorganica Chimica Acta, 359(10): 3257-3263, (2006). DOI: https://doi.org/10.1016/j.ica.2006.03.038
Adams, E.J., Skrydstrup. T., Lindsay, K.B., “2-Pyridinethiol, Encyclopedia of Reagents for Organic Synthesis”, (2005). DOI: https://doi.org/10.1002/047084289X.rp286
Shunmugam, R., Sathyanarayana, D.N., “Raman and polarized infrared spectra of pyridine-2-thione”, Spectrochimica Acta Part A: Molecular Spectroscopy, 40(8):757-761, (1984). DOI: https://doi.org/10.1016/0584-8539(84)80100-2
Castiñiras, A., Hiller, W., Strähle, J., Bravo, J., Casas, J., Gayoso, M., Sordo, J., “Methyl- and phenyl-mercury(II) derivatives of 2-mercaptopyridine. Crystal and molecular structure of methyl(pyridine-2-thiolato)mercury(II)”, Journal of the Chemical Society, Dalton Transactions, 9:1945-1948, (1986). DOI: https://doi.org/10.1039/dt9860001945
Toma, H.E., Santos, P.S., Mattioli, M.P.D., Oliveira, L.A.A., “Kinetics, electrochemistry and resonance raman spectra of the (2-mercaptopyridine) (edta)ruthenium(III) complex”, Polyhedron, 6(3): 603-611, (1987). DOI: https://doi.org/10.1016/S0277-5387(00)81031-1
Baldwin, J.A., Vlčková, B., Andrews, M.P., Butler, S., “Surface-Enhanced Raman Scattering of Mercaptopyridines and Pyrazinamide Incorporated in Silver Colloid−Adsorbate Films”, Langmuir, 13(14):3744-3751, (1997). DOI: https://doi.org/10.1021/la960719d
Pang, Y.S., Hwang, H.J., Kim, M.S., “Adsorption of 2-mercaptopyridine and 2-mercaptopyrimidine on a silver colloidal surface investigated by Raman spectroscopy”, Journal of Molecular Structure, 441(1): 63-76, (1998). DOI: https://doi.org/10.1016/s0022-2860(97)00280-9
Zhang, H.L., Evans, S.D., Henderson, J.R., Miles, R.E., Shen, T.H., “Spectroscopic Characterization of Gold Nanoparticles Passivated by Mercaptopyridine and Mercaptopyrimidine Derivatives”, The Journal of Physical Chemistry B, 107(25): 6087-6095, (2003). DOI: https://doi.org/ 10.1002/Adma.200390124
Ozturk, I.I., Kourkoumelis, N., Hadjikakou, S.K., Manos, M.J., Tasiopoulos, A.J., Butler, I.S., Balzarini, J., Hadjiliadis, N., “Interaction of antimony(III) chloride with thiourea, 2-mercapto-5-methyl-benzimidazole, 3-methyl-2-mercaptobenzothiazole, 2-mercaptopyrimidine, and 2-mercaptopyridine”, Journal of Coordination Chemistry, 64(22): 3859-3871, (2011). DOI: https://doi.org/10.1080/00958972.2011.633603
Do, W.H., Lee, C.J., Kim, D.Y., Jung, M.J., “Adsorption of 2-mercaptopyridine and 4-mercaptopyridine on a silver surfaces investigated by SERS spectroscopy”, Journal of Industrial and Engineering Chemistry, 18(6): 2141-2146, (2012). DOI: https://doi.org/10.1016/j.jiec.2012.06.009
Naktode, K., Reddy, T.D.N., Nayek, H.P., Mallik, B.S., Panda, T.K., “Heavier group 2 metal complexes with a flexible scorpionate ligand based on 2-mercaptopyridine”, Royal Society of Chemistry Advances, 5(63): 51413-51420, (2015). DOI: https://doi.org/10.1039/C5RA04696C
Ramsay, D.A., “The Vibration Spectrum and Molecular Configuration of 1,4-dioxane”. Proceedings of the Royal Society of London A, 190: 562-574, (1947). DOI: https://doi.org/10.1098/rspa.1947.0097
Malherbe, F.E., Bernstein, H.J., “The Infrared and Raman Spectra of p-Dioxane”, Journal of the American Chemical Society, 74(17): 4408-4410, (1952). DOI: https://doi.org/10.1021/ja01137a051
Snyder, R.G., Zerbi, G., “Vibrational analysis of ten simple aliphatic ethers: Spectra, assignments, valence force field and molecular conformations”, Spectrochimica Acta Part A: Molecular Spectroscopy, 23(2): 391-437, (1967). DOI: https://doi.org/10.1016/0584-8539(67)80241-1
Ellestad, O.H., Klaboe, P., Hagen, G., “The vibrational spectra of 1,4-dioxan-do and 1,4- dioxan-d8”, Spectrochimica Acta, 27A: 1025-1048, (1971). DOI: https://doi.org/10.1016/0584-8539(71)80186-1
Karayannis, N.M., Mikulski, C.M., Speca, A.N., Cronin, J.T., Pytlewski, L.L., “p-Dioxane, p-thioxane, and 1,2-dimethoxyethane complexes with transition metal perchlorates”, Inorganic Chemistry, 11(10): 2330-2335, (1972). DOI: https://doi.org/10.1021/ic50116a008
Shimanouchi, T., “Tables of molecular vibrational frequencies consolidated volume II”, Journal of Physical and Chemical Reference Data., 6(3): 993-1102, (1977). DOI: https://doi.org/10.1063/1.555560
Schwarz, W., Schmidt, A., Binder, G.E., “1,4-Dioxan•H2O•SbCl5; Vibrational Spectra, Crystal and Molecular Structure”, Zeitschrift für Naturforschung B, 33(2): 136-139, (1978). DOI: https://doi.org/10.1515/znb-1978-0202
Dempster, A.B., Uslu, H., “Infrared spectra and stability of Hofmann-type dioxane clathrates”, Spectrochimica Acta Part A: Molecular Spectroscopy, 34(1): 71-75, (1978). DOI: https://doi.org/10.1016/0584-8539(78)80188-3
Den, H.M., Driessen, W.L., “Ethers as ligands, Part IV, Metal(II) 1,4-dioxane solvates”, Inorganica Chimica Acta, 39:43-46, (1980). DOI: https://doi.org/10.1016/s0020-1693(00)93631-4
Parvez, M., Pajerski, A.D., Richey, H.G., “(Dioxane)dineopentylmagnesium: a polymeric structure”, Acta Crystallographica Section C Crystal Structure Communications, 44(7): 1212-1215, (1998). DOI: https://doi.org/10.1107/s0108270188003099
Edelmann, F.T., Pauer, F., Wedler, M., Stalke, D., “Preparation and structural characterization of dioxane-coordinated alkali metal bis(trimethylsilyl)amides”, Inorganic Chemistry, 31(20): 4143-4146, (1992). DOI: https://doi.org/10.1021/ic00046a028
Parlak, C., Alver, Ö., “Spectroscopic investigations of 1,4-dioxane adsorbed on bentonite from Anatolia”, Anadolu University Journal of Science and Technology A - Applied Sciences and Engineering, 17(2): 273-277, (2016). DOI: https://doi.org/10.18038/btda,87236
Borowski, P., Gac, W., Pulay, P., Wolinski, K., “The vibrational spectrum of 1,4-dioxane in aqueous solution – theory and experiment”, New Journal of Chemistry, 40(9): 7663-7670, (2016). DOI: https://doi.org/10.1039/c6nj01198e
Kartal, Z., Yavuz, A., “The synthesis and the spectroscopic, thermal, and structural properties of the M2[(fumarate)Ni(CN)4]•2(1,4-Dioxane) clathrate (M = Co, Ni, Cd and Hg)”, Journal of Molecular Structure, 1155: 171-183, (2018). DOI: https://doi.org/10.1016/j.molstruc.2017.10.107
Lockwood, D.J., Bertrand, D., Carrara, P., Mischler, G., Billerey, D., Terrier, C., “Raman spectrum of NiCl2”, Journal of Physics C: Solid State Physics, 11(17): 3615-3620, (1979). DOI: https://doi.org/10.1088/0022-3719/12/17/031
Agulló-Rueda, F., Calleja, J.M., Martini, M., Spinolo, G., Cariati, F., “Raman and infrared spectra of transition metal halide hexahydrates”, Journal of Raman Spectroscopy, 18(7): 485-491, (1987). DOI: https://doi.org/10.1002/jrs.1250180707
Lide, D.R., “CRC Handbook of Chemistry and Physics”, 90th ed, Boca Raton, Florida, USA: CRC Press, ISBN 978-1-4200-9084-0, (2009).
Seidell, A., “Solubilities of Inorganic and Organic Compounds: A Compilation of Quantitave Solubility Data From the Periodical Literature; Volume 1”, Legare Street Press, ISBN-10: 1015948987, (2022).
Greenwood, N.N., Earnshaw, A., “Chemistry of the Elements”, 2nd ed, Butterworth-Heinemann, Oxford, UK: ISBN: 9780750633659. (1997).
Young, D.C., “Computational chemistry: a practical guide for applying techniques to real-world problems (electronics)”, New York, USA: Wiley, ISBN: 0-471-33368-9, (2001).
Dennington, R., Keith, T., Millam, J., Gauss View, Version 4.1.2. Semichem Inc., Shawnee Mission (2007).
Macrae, C.F., Bruno, I.J., Chisholm, J.A., Edgington, P., McCabe, P., Pidcock, E., Rodriguez-Monge, L., Taylor, R., van de Streek, J., Wood, P.A., “Mercury CSD 2.0 – New features for the visualization and investigation of crystal structures”, Journal of Applied Crystallography, 41: 466-470, (2008). DOI: https://doi.org/10.1107/S0021889807067908
Sickerman, N.S., Park, Y.J., Ng, G.K.Y., Bates, J.E. Hilkert, M., Ziller, J.W., Furche, F., Borovik, A.S., “Synthesis, structure, and physical properties for a series of trigonal bipyramidal M(II)-Cl complexes with intramolecular hydrogen bonds”, Dalton Transactions, 41(15): 4358-4364, (2012). DOI: https://doi.org/10.1039/c2dt12244h
Gusev, A.N., Shul’gin, V.F., Ryush, I.O., Hasegawa, M., Kiskin, M.A., Efimov, N.N., Konstantin, A., Lyssenko, A., Eremenko, I.L., Linert, W., “Copper(II), Nickel(II), and Cobalt(II)/(III) Self-Assembled Polynuclear Complexes of Bis[(pyridin-2-yl)-1,2,4-triazol-3-yl]]methane”, European Journal of Inorganic Chemistry, 3: 704-712, (2017). DOI: https://doi.org/10.1002/ejic.201601107
Paes, L.W.C., Suárez, J.A., Márquez, A.M., Sanz, J.F., “First-principles study of nickel complex with 1,3-dithiole-2-thione-4,5-dithiolate ligands as model photosensitizers”, Theoretical Chemistry Accounts, 136(6): 1-9, (2017). DOI: https://doi.org/10.1007/s00214-017-2098-7
Hakimi, M., Mardani, Z., Moeini, K., Fernandes, M.A., “Coordination geometries and crystal structures of cadmium(II) complexes with a new amino alcohol (NN′O) ligand”, Journal of Coordination Chemistry, 65(13): 2221-2233, (2012). DOI: https://doi.org/10.1080/00958972.2012.690145
Kawasaki, T., Kitazawa, T., “Synthesis and Crystal Structures of Cadmium(II) Cyanide with Branched-Butoxyethanol”, Crystals, 8(5): 221/1-221/10, (2018). https://doi.org/10.3390/cryst8050221
BelhajSalah, S., Abdelbaky, M.S.M., García-Granda, S., Essalah, K., Ben Nasr, C., Mrad, M.L., “Crystal structure, Hirshfeld surfaces computational study and physicochemical characterization of the hybrid material (C7H10N)2[SnCl6]•H2O”, Journal of Molecular Structure, 1152: 276-286, (2018). DOI: https://doi.org/10.1016/j.molstruc.2017.09.098
Jellali, A., Elleuch, S., Hamdi, B., Zouari, R., “Experimental and theoretical investigations of the molecular structure, the spectroscopic properties and TD-DFT analysis of a new semiconductor hybrid based iron (III)”, Journal of Saudi Chemical Society, 23(5): 600-611, (2019). DOI: https://doi.org/10.1016/j.jscs.2018.10.006
Zhang, W., Schmid, T., Yeo, B.S., Zenobi, R., “Tip-enhanced Raman spectroscopy reveals rich nanoscale adsorption chemistry of 2-mercaptopyridine on Ag”, Israel Journal of Chemistry, 47(2): 177-184, (2007). DOI: https://doi.org/10.1560/ijc.47.2.177
Kartal, Z., Sayın, E., “FTIR spectroscopic and thermal study of M(Cyclohexanethiol)2Ni(CN)4•(1,4-dioxane) clathrate (M = Mn, Co, Ni and Cd)”, Journal of Molecular Structure, 994(1-3): 170-178, (2011). DOI: https://doi.org/10.1016/j.molstruc.2011.03.014
Kartal, Z., Türk, T., “FT-IR spectroscopic and thermal study of M(1,6-hexanedithiol)Ni(CN)4⋅2(1,4-dioxane) clathrate (M = Mn, Co, Ni and Cd)”, Journal of Molecular Structure, 1014: 74-80, (2012). DOI: https://doi.org/10.1016/j.molstruc.2012.01.031
Eckert, S., Miedema, P.S., Quevedo, W., O’Cinneide, B., Fondell, M., Beye, M., Pietzsch, A., Ross, M., Khalil, M., Föhlisch, A., “Molecular structures and protonation state of 2-Mercaptopyridine in aqueous solution”, Chemical Physics Letters, 647: 103-106, (2016). DOI: https://doi.org/10.1016/j.cplett.2016.01.050
Do, W.H., Lee, C.J., Kim, D.Y., Jung, M.J., “Adsorption of 2-mercaptopyridine and 4-mercaptopyridine on a silver surfaces investigated by SERS spectroscopy”, Journal of Industrial and Engineering Chemistry, 18(6): 2141-2146, (2012). DOI: https://doi.org/10.1016/j.jiec.2012.06.009
Jamroz, M.H., “Vibrational Energy Distribution Analysis VEDA 4”, Warsaw, (2004-2010).
Solomons, T.W.G., Fryhle, C.B., Scott, A., “Organic Chemistry”, New York, USA: Wiley, ISBN 10: 1119768195, (2022).
Lockwood, D.J., “Raman Spectra of Cadmium Chloride and Cadmium Bromide. In: G.B. Wright (eds) Light Scattering Spectra of Solids”, Springer, Berlin, Heidelberg, (1969). DOI: https://doi:10.1007/978-3-642-87357-7_6
Lockwood, D.J., “Lattice vibrations of CdCl2, CdBr2, MnCl2, and CoCl2: infrared and Raman spectra”, Journal of the Optical Society of America, 63: 374-382, (1973). DOI: https://doi.org/10.1364/JOSA.63.000374