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Ab-initio Study Aiming Some Spectroscopic and Electronic Properties of 2-[(1H-benzimidazol-1-yl)- methyl]benzoic acid

Year 2022, Volume: 4 Issue: 2, 209 - 223, 31.12.2022

Abstract

In this study, our main aim to characterize the title molecule of C15H12N2O2 by using quantum chemistry computational method. We have performed ab-initio simulations to determine the quantized energy levels of molecules, ions or nuclei, which enable to obtain its structural parameters and, some spectroscopic, electronic and thermal properties. The compound is optimized by using ab-initio method based on the density functional theory (DFT)/B3LYP with 6-31G(d,p) basis set implemented in Gaussian 09W subprogram. The geometric parameters of bond length, bond angle and dihedral angle computed are in good agreement with those of available experiment. The same basis set and computational method have been utilized for the vibrational spectra of the title compound by using the optimized structure. The marking of the vibrational frequencies of the molecule have been carried out via the VEDA4 program (Vibrational Energy Distribution Analysis). The title molecule has 31 atoms and 87 fundamental vibrational modes, with the most bending vibrations. Since experimental chemical shifts are generally obtained in DMSO (Dimethyl Sulfoxide) and Acetonitrile solutions, the 1H and 13C NMR chemical shifts of the molecule in the same solutions are computed by using the Gauge-Independent Atomic Orbital (GIAO) approach applying DFT/B3LYP method with the basis set of 6-31G (d,p). Moreover, UV-Vis spectral analysis of the studied molecule have been investigated in both of the DMSO and Acetonitrile solvents. The maximum absorption peaks of compound have been evaluated by the Time Dependent Self-Consistent Field (TD-SCF)/DFT/B3LYP/6-31G(d,p) method. A single absorbance without any shoulder at 257 nm in both solvent have been observed. At last, electronic properties such as chemical hardness/softness, ionization potential, highest occupied molecular orbital (HOMO)-lowest unoccupied molecular orbital (LUMO) energy levels, electronegativity and energy bandgap have been predicted. Our results from DFT calculations not only aid in the interpretation of available experimental data, but also illuminate the spectroscopic and electronic properties of the title molecule in detail.

Supporting Institution

Pamukkale University

Project Number

2018FEBE052

References

  • Aboraia A. S., Abdel-Rahman H. M., Mahfouz N. M., & El-Gendy M. A. 2006. Novel 5-(2-hydroxyphenyl)-3-substituted-2, 3-dihydro-1, 3, 4-oxadiazole-2-thione derivatives: Promising anticancer agents. Bioorganic & medicinal chemistry, 14(4), 1236-1246.
  • Ali A., Muslim M., Kamaal S., Ahmed A., Ahmad M., Shahid M., ... & Mashrai A. 2021. Crystal structure, Hirshfeld and electronic transition analysis of 2-[(1H-benzimidazol-1-yl) methyl] benzoic acid. Acta Crystallographica Section E: Crystallographic Communications, 77(7), 755-758.
  • Bansal R. 2007. Heterocyclic chemistry. 4th ed. Tunbridge Wells: Anshan Ltd; p. 1-2.
  • Becke A. D. 1992. Density‐functional thermochemistry. I. The effect of the exchange‐only gradient correction. The Journal of chemical physics, 96(3), 2155-2160. Boiani M., & González M. 2005. Imidazole and benzimidazole derivatives as chemotherapeutic agents. Mini reviews in medicinal chemistry, 5(4), 409-424.
  • Castilloa R. 2002. Synthesis and antiparasitic activity of 1H-benzimidazole derivatives. Bioorg. Med. Chem. Lett., 12, 2221–2224.
  • Dennington R., Keith T., & Millam J. 2009. Semichem Inc. Shawnee Mission KS, GaussView, Version, 5.
  • Ditchfield R. 1972. Molecular orbital theory of magnetic shielding and magnetic susceptibility. The Journal of Chemical Physics, 56(11), 5688-5691.
  • Edwin B., & Joe I. H. 2013. Vibrational spectral analysis of anti-neurodegenerative drug Levodopa: A DFT study. Journal of Molecular Structure, 1034, 119-127.
  • Frisch M., Trucks G. W., Schlegel H. B., Scuseria G. E., Robb M. A., Cheeseman J. R., ... & Fox, D. J. 2009. Gaussian 09. Gaussian Inc. Wallingford CT, 106.
  • Hohenberg P., & Kohn W. 1964. Inhomogeneous electron gas. Physical review, 136(3B), B864.
  • Jamróz M. H. 2013. Vibrational energy distribution analysis (VEDA): scopes and limitations. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 114, 220-230.
  • Jeyavijayan S., & Arivazhagan M. 2010. Study of density functional theory and vibrational spectra of hypoxanthine. Indian J. Pure Appl. Phys. 2010, 48, 869–874.
  • Johnson III, R. D. 2013. NIST computational chemistry comparison and benchmark database, NIST standard reference database number 101. Release 16a http://cccbdb. nist. gov/(accessed Mar 13, 2021).
  • Khanum G., Ali A., Shabbir S., Fatima A., Alsaiari N., Fatima Y., Ahmad M., Siddiqui N., Javed S., Gupta M. 2022. Vibrational Spectroscopy, Quantum Computational and Molecular Docking Studies on 2-[(1H-benzimidazol-1-yl)-methyl] benzoic acid. Crystals, 12(3), 337.
  • Kumar D., Jacob, M.R., Reynolds, M.B., Kerwin, S.M. (2002. Synthesis and evaluation of anticancer benzoxazoles and benzimidazoles related to UK-1, Bioorg.Med.Chem., vol. 10, pp. 3997–4004, 2002.
  • Özbey S., Ide S., Kendi E. 1998. The crystal and molecular structure of two benzimidazole derivatives: (phenylmethyl)-2-(4-methoxyphenylmethyl)-1H-benzimidazole-5-carboxylic acid (I) and 1,2-di-(phenylmethyl)-1H-benzimidazole-5-carboxylic acid (II)”, Journal of Molecular Structure, vol. 442, pp. 23-30,1998.
  • Palosi E. Dezso K. Erzsebet M., Szvoboda I., Laszlo H., Gyorgy S., Sandor V., Vera Katalin M. 1990. European Patent Appl. EP. 324, 988, Chem. Abstr., vol. 112, pp. 55864.
  • Ramanatham V., Sanjay D.V., Kumar B.V.S., Umesh N.B., Shekar B.B., Mashelkar U.C. 2008. Synthesis, anti-bacterial, antiasthmatic and anti-diabetic activities of novel N-substituted 2-(4-styrylphenyl)-1H-benzimidazole and N-substituted-3[4-(1H-benzimidazole-2-yl)-phenyl]-acrylic acid tert-butyl ester. ARKIVOC, 10, 37–49.
  • Saş, E. B., Kurt M., Can M., Okur S., İçli S., & Demiç S. 2014. Structural investigation of a self-assembled monolayer material 5-[(3-methylphenyl)(phenyl) amino] isophthalic acid for organic light-emitting devices. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 133, 307-317.
  • Sastri V. S., & Perumareddi J. R. 1997. Molecular orbital theoretical studies of some organic corrosion inhibitors. Corrosion, 53(08).
  • Sudha S., Karabacak M., Kurt M., Cınar M., Sundaraganesan N. 2010. Molecular structure, vibrational spectroscopic, first-order hyperpolarizability and HOMO, LUMO studies of 2-amino benzimidazole, Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, vol.84, pp. 184-195, 2010.
  • Sundaraganesan N., Ilakiamani S., Subramani P., & Joshua B. D. 2007. Comparison of experimental and ab initio HF and DFT vibrational spectra of benzimidazole. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 67(3-4), 628-635.
  • Wade L.G. (Ed.).1992. Advanced Organic Chemistry, 4th ed.;Wiley: New York, NY, USA, 1992; pp. 723–729.
  • Wolinski K., Hinton J. F., & Pulay P. 1990. Efficient implementation of the gauge-independent atomic orbital method for NMR chemical shift calculations. Journal of the American Chemical Society, 112(23), 8251-8260.
  • Valdez J., Cedillo R., Hernandez-Campos A., Yepez L., Hernandez-Luis F., Navarrete-Vazquez G., Tapia A., Cortes R., Hernandezc M.,
  • Varsányi G., Kovner M. A., & Láng L. 1973. Assignments for vibrational spectra of 700 benzene derivatives. Akademiai Kiado.

2-[(1H-benzimidazol-1-il)-metil]benzoik asit Molekülüne Ait Bazı Spektroskopik ve Elektronik Özellikleri Üzerine Ab-initio Çalışması

Year 2022, Volume: 4 Issue: 2, 209 - 223, 31.12.2022

Abstract

u çalışmada temel amacımız, kuantum kimyası hesaplama yöntemini kullanarak C15H12N2O2 başlık molekülünü karakterize etmektir. Moleküllerin, iyonların veya çekirdeklerin, yapısal parametrelerinin ve bazı spektroskopik, elektronik ve termal özelliklerinin elde edilmesini sağlayan nicelleştirilmiş enerji seviyelerini belirlemek için ab-initio simülasyonları gerçekleştirdik. Bileşik, Gaussian 09W alt programında uygulanan 6-31G(d,p) temel seti ile yoğunluk fonksiyonel teorisi (DFT)/B3LYP'ye dayalı ab-initio yöntemi kullanılarak optimize edilmiştir. Hesaplanan bağ uzunluğu, bağ açısı ve dihedral açının geometrik parametreleri, mevcut deneyinkilerle iyi bir uyum içindedir. Optimize edilmiş yapı kullanılarak başlık bileşiğinin titreşim spektrumları için aynı temel set ve hesaplama yöntemi kullanılmıştır. Molekülün titreşim frekanslarının işaretlenmesi VEDA4 programı (Vibrational Energy Distribution Analysis) ile yapılmıştır. Başlık molekülü 31 atoma ve en çok bükülme titreşimine sahip 87 temel titreşim moduna sahiptir. Deneysel kimyasal kaymalar genellikle DMSO (Dimetil Sülfoksit) ve Asetonitril çözeltilerinde elde edildiğinden, molekülün aynı çözeltilerdeki 1H ve 13C NMR kimyasal kaymaları DFT/B3LYP yöntemi uygulanarak Gauge-Bağımsız Atomik Yörünge (GIAO) yaklaşımı kullanılarak hesaplanmıştır. 6-31G (d,p) temel seti ile. Ayrıca, çalışılan molekülün UV-Vis spektral analizi hem DMSO hem de Asetonitril çözücülerde araştırılmıştır. Bileşiğin maksimum absorpsiyon zirveleri, Zamana Bağlı Kendinden Tutarlı Alan (TD-SCF)/DFT/B3LYP/6-31G(d,p) yöntemi ile değerlendirilmiştir. Her iki çözücüde de 257 nm'de herhangi bir omuz olmaksızın tek bir absorbans gözlenmiştir. Son olarak, kimyasal sertlik/yumuşaklık, iyonlaşma potansiyeli, en yüksek dolu moleküler orbital (HOMO)-en düşük boş moleküler orbital (LUMO) enerji seviyeleri, elektronegatiflik ve enerji bant aralığı gibi elektronik özellikler tahmin edilmiştir. DFT hesaplamalarından elde ettiğimiz sonuçlar, yalnızca mevcut deneysel verilerin yorumlanmasına yardımcı olmakla kalmaz, aynı zamanda başlık molekülünün spektroskopik ve elektronik özelliklerini ayrıntılı olarak aydınlatır.

Project Number

2018FEBE052

References

  • Aboraia A. S., Abdel-Rahman H. M., Mahfouz N. M., & El-Gendy M. A. 2006. Novel 5-(2-hydroxyphenyl)-3-substituted-2, 3-dihydro-1, 3, 4-oxadiazole-2-thione derivatives: Promising anticancer agents. Bioorganic & medicinal chemistry, 14(4), 1236-1246.
  • Ali A., Muslim M., Kamaal S., Ahmed A., Ahmad M., Shahid M., ... & Mashrai A. 2021. Crystal structure, Hirshfeld and electronic transition analysis of 2-[(1H-benzimidazol-1-yl) methyl] benzoic acid. Acta Crystallographica Section E: Crystallographic Communications, 77(7), 755-758.
  • Bansal R. 2007. Heterocyclic chemistry. 4th ed. Tunbridge Wells: Anshan Ltd; p. 1-2.
  • Becke A. D. 1992. Density‐functional thermochemistry. I. The effect of the exchange‐only gradient correction. The Journal of chemical physics, 96(3), 2155-2160. Boiani M., & González M. 2005. Imidazole and benzimidazole derivatives as chemotherapeutic agents. Mini reviews in medicinal chemistry, 5(4), 409-424.
  • Castilloa R. 2002. Synthesis and antiparasitic activity of 1H-benzimidazole derivatives. Bioorg. Med. Chem. Lett., 12, 2221–2224.
  • Dennington R., Keith T., & Millam J. 2009. Semichem Inc. Shawnee Mission KS, GaussView, Version, 5.
  • Ditchfield R. 1972. Molecular orbital theory of magnetic shielding and magnetic susceptibility. The Journal of Chemical Physics, 56(11), 5688-5691.
  • Edwin B., & Joe I. H. 2013. Vibrational spectral analysis of anti-neurodegenerative drug Levodopa: A DFT study. Journal of Molecular Structure, 1034, 119-127.
  • Frisch M., Trucks G. W., Schlegel H. B., Scuseria G. E., Robb M. A., Cheeseman J. R., ... & Fox, D. J. 2009. Gaussian 09. Gaussian Inc. Wallingford CT, 106.
  • Hohenberg P., & Kohn W. 1964. Inhomogeneous electron gas. Physical review, 136(3B), B864.
  • Jamróz M. H. 2013. Vibrational energy distribution analysis (VEDA): scopes and limitations. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 114, 220-230.
  • Jeyavijayan S., & Arivazhagan M. 2010. Study of density functional theory and vibrational spectra of hypoxanthine. Indian J. Pure Appl. Phys. 2010, 48, 869–874.
  • Johnson III, R. D. 2013. NIST computational chemistry comparison and benchmark database, NIST standard reference database number 101. Release 16a http://cccbdb. nist. gov/(accessed Mar 13, 2021).
  • Khanum G., Ali A., Shabbir S., Fatima A., Alsaiari N., Fatima Y., Ahmad M., Siddiqui N., Javed S., Gupta M. 2022. Vibrational Spectroscopy, Quantum Computational and Molecular Docking Studies on 2-[(1H-benzimidazol-1-yl)-methyl] benzoic acid. Crystals, 12(3), 337.
  • Kumar D., Jacob, M.R., Reynolds, M.B., Kerwin, S.M. (2002. Synthesis and evaluation of anticancer benzoxazoles and benzimidazoles related to UK-1, Bioorg.Med.Chem., vol. 10, pp. 3997–4004, 2002.
  • Özbey S., Ide S., Kendi E. 1998. The crystal and molecular structure of two benzimidazole derivatives: (phenylmethyl)-2-(4-methoxyphenylmethyl)-1H-benzimidazole-5-carboxylic acid (I) and 1,2-di-(phenylmethyl)-1H-benzimidazole-5-carboxylic acid (II)”, Journal of Molecular Structure, vol. 442, pp. 23-30,1998.
  • Palosi E. Dezso K. Erzsebet M., Szvoboda I., Laszlo H., Gyorgy S., Sandor V., Vera Katalin M. 1990. European Patent Appl. EP. 324, 988, Chem. Abstr., vol. 112, pp. 55864.
  • Ramanatham V., Sanjay D.V., Kumar B.V.S., Umesh N.B., Shekar B.B., Mashelkar U.C. 2008. Synthesis, anti-bacterial, antiasthmatic and anti-diabetic activities of novel N-substituted 2-(4-styrylphenyl)-1H-benzimidazole and N-substituted-3[4-(1H-benzimidazole-2-yl)-phenyl]-acrylic acid tert-butyl ester. ARKIVOC, 10, 37–49.
  • Saş, E. B., Kurt M., Can M., Okur S., İçli S., & Demiç S. 2014. Structural investigation of a self-assembled monolayer material 5-[(3-methylphenyl)(phenyl) amino] isophthalic acid for organic light-emitting devices. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 133, 307-317.
  • Sastri V. S., & Perumareddi J. R. 1997. Molecular orbital theoretical studies of some organic corrosion inhibitors. Corrosion, 53(08).
  • Sudha S., Karabacak M., Kurt M., Cınar M., Sundaraganesan N. 2010. Molecular structure, vibrational spectroscopic, first-order hyperpolarizability and HOMO, LUMO studies of 2-amino benzimidazole, Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, vol.84, pp. 184-195, 2010.
  • Sundaraganesan N., Ilakiamani S., Subramani P., & Joshua B. D. 2007. Comparison of experimental and ab initio HF and DFT vibrational spectra of benzimidazole. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 67(3-4), 628-635.
  • Wade L.G. (Ed.).1992. Advanced Organic Chemistry, 4th ed.;Wiley: New York, NY, USA, 1992; pp. 723–729.
  • Wolinski K., Hinton J. F., & Pulay P. 1990. Efficient implementation of the gauge-independent atomic orbital method for NMR chemical shift calculations. Journal of the American Chemical Society, 112(23), 8251-8260.
  • Valdez J., Cedillo R., Hernandez-Campos A., Yepez L., Hernandez-Luis F., Navarrete-Vazquez G., Tapia A., Cortes R., Hernandezc M.,
  • Varsányi G., Kovner M. A., & Láng L. 1973. Assignments for vibrational spectra of 700 benzene derivatives. Akademiai Kiado.
There are 26 citations in total.

Details

Primary Language English
Subjects Atomic, Molecular and Optical Physics, Nonlinear Optics and Spectroscopy
Journal Section Articles
Authors

Eylem Çelik 0000-0002-3941-1793

Pinar Tasli 0000-0001-6580-9765

Sevgi Özdemir Kart 0000-0001-5706-7722

Project Number 2018FEBE052
Early Pub Date December 25, 2022
Publication Date December 31, 2022
Submission Date June 15, 2022
Acceptance Date December 21, 2022
Published in Issue Year 2022 Volume: 4 Issue: 2

Cite

APA Çelik, E., Tasli, P., & Özdemir Kart, S. (2022). Ab-initio Study Aiming Some Spectroscopic and Electronic Properties of 2-[(1H-benzimidazol-1-yl)- methyl]benzoic acid. Journal of Spectroscopy and Molecular Sciences, 4(2), 209-223.