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Bazı yeni N-sübstitüe amino asit esterlerinin yapısal özelliklerinin in silico ile araştırılması

Yıl 2023, Cilt: 25 Sayı: 2, 748 - 760, 07.07.2023

Ümit Çalışır Baki Çiçek

https://doi.org/10.25092/baunfbed.1310449

Öz

Bu çalışma kapsamında oldukça önemli biyolojik kullanım alanlarına sahip N-sübstitüe glisin ester bileşiklerinin bazı teorik (hesapsal) özellikleri HyperChem programı yardımıyla hesaplanmıştır. HyperChem programı kullanılarak etil 9-{[(2-etoksi-2-oksoetil)amino]etil}-4-okso-3-oksa-6,9,12-triazatetradekan-14-oat (1), dietil 3,6,9,12,15-pentaazaheptadekan-1,17-dioat (2), ve etil 2-((6-metil-2-piridinil)amino)asetat (3) bileşiklerinin bağ uzunlukları, toplam yük yoğunluğu ve yük dağılımı, elektrostatik potansiyelleri belirlenmiştir. En kararlı yapıları üzerinden bazı enerji parametreleri ile HOMO, LUMO, ve ΔE orbitalleri hesaplanmıştır. Elde edilen verilerden yararlanılarak iyonlaşma potansiyeli belirlenmiştir. Ayrıca teorik elektronik UV spektrumu ve geçiş değerleri hesaplanmıştır. Bu yöntemle hesaplanmış teorik UV spektrumu ve geçiş değerleri, deneysel olarak elde edilen UV-VİS spektrumu karşılaştırılarak kıyaslanmıştır. Teorik ve deneysel verilerin uyumlu oldukları tespit edilmiştir. Bileşiklerin reaktivitesi ile ilişkili olan ΔE değerinin, (3) bileşiğinde oldukça düşük olduğu belirlenmiştir (8.8559 eV).

Anahtar Kelimeler

N-sübstitüe amino asit esterleri in silico HyperChem teorik (hesapsal) kimya

Kaynakça

  • Çalışır, Ü. ve Çiçek, B., Synthesis, characterization and determination of some theoretical properties of ethyl 2-((4,6-dimethylpyrimidin-2- yl)amino)acetate, Proceedings, III. International Siirt Conference on Scientific, 686–696, ISPEC Publishing House, (2022).
  • Culf, A. S. ve Ouellette, R. J., Solid-phase synthesis of N-substituted glycine oligomers (alpha-peptoids) and derivatives, Molecules, 15, 5282–5335, (2010).
  • Seo, J., Lee, B.-C. ve Zuckermann, R. N., Peptoids: Synthesis, Characterization, and Nanostructures, Comprehensive Biomaterials, 53–76, Elsevier, (2011).
  • Wetzer, M., Kapoor, R., Huang, W. ve Barron, A. E., Peptoid Oligomers: Peptidomimetics for Diverse Biomedical Applications, Polymer Science: A Comprehensive Reference, 267–287, Elsevier, (2012).
  • Bolt, H. L., Kleijn, L. H. J., Martin, N. I. ve Cobb, S. L., Synthesis of antibacterial nisin–peptoid hybrids using click methodology, Molecules, 23, 1–9, (2018).
  • Zuckermann, R. N., et al., Discovery of nanomolar ligands for 7-transmembrane G-protein-coupled receptors from a diverse N-(substituted)glycine peptoid library, Journal of Medicinal Chemistry, 37, 2678–2685, (1994).
  • Pospíšil, Š., et al., Epigenetic pyrimidine nucleotides in competition with natural dNTPs as substrates for diverse DNA polymerases, ACS Chemical Biology, 17, 2781–2788, (2022).
  • House, D. A., Ammonia \ N-donor ligands, Encyclopedia of Inorganic Chemistry, John Wiley & Sons Ltd, (2006).
  • Sigma Aldrich, Tris(2-aminoethyl)amine, Sigma Aldrich Co., (2022).
  • Pawlaczyk, M. ve Schroeder, G., Adsorption studies of Cu(II) ions on dendrimer-grafted silica-based materials, Journal of Molecular Liquids, 281, 176–185, (2019).
  • Fan, Y., et al., Synthesis and aggregation behavior of a hexameric quaternary ammonium surfactant, Langmuir, 27, 10570–10579, (2011).
  • Patras, G., Qiao, G. G., Solomon, D. H. ve Koch, R., Synthesis, characterization, and modelling of novel multifunctional acryloyl-based monomers: an experimental and computational study, Australian Journal of Chemistry, 55, 675–680, (2002).
  • Afrin, R., Shah, N. A., Abbas, M., Amin, M. ve Bhatti, A. S., Sensors and actuators A : Physical design and analysis of functional multiwalled carbon nanotubes for infrared sensors, Sensors Actuators A, 203, 203, 142–148, (2013).
  • Vasil’eva, S. V., Abramova, T. V., Ivanova, T. M., Shishkin, G. V. ve Sil’nikov, V. N., Monomers for oligonucleotide synthesis with linkers carrying reactive residues: II. The synthesis of phosphoamidites on the basis of uridine and cytosine and containing a linker with methoxyoxalamide groups in position 2′, Russian Journal of Bioorganic Chemistry, 30, 234–242, (2004).
  • Zain-ul-Abdin et al, Tris(2-aminoethyl)amine-based ferrocene-terminated dendrimers as burning rate catalysts for ammonium perchlorate-based propellant decomposition, Applied Organometallic Chemistry, 32, 1–11, (2018).
  • Rawal, R. K., Dutta, B. ve Patel, P., Pyrimidine ring containing natural products and their biological importance, Pyrimidines And Their Importance, Nova Science Publishers, (2023).
  • Lagoja, I. M., Pyrimidine as constituent of natural biologically active compounds. Chemistry & Biodiversity, 2, 1–50, (2005).
  • Madhavan, G. R., et al., Synthesis and biological activity of novel pyrimidinone containing thiazolidinedione derivatives, Bioorganic & Medicinal Chemistry, 10, 2671–2680, (2002).
  • Gichinga, M. G., et al., Synthesis and evaluation of metabotropic glutamate receptor subtype 5 antagonists based on fenobam, ACS Medicinal Chemistry Letters, 2, 882–884, (2011).
  • Pretorius, S. I., Breytenbach, W. J., de Kock, C., Smith, P. J. ve N’Da, D. D., Synthesis, characterization and antimalarial activity of quinoline-pyrimidine hybrids, Bioorganic & Medicinal Chemistry, 21, 269–277, (2013).
  • Zuniga, E. S., et al., The synthesis and evaluation of triazolopyrimidines as anti-tubercular agents, Bioorganic & Medicinal Chemistry, 25, 3922–3946, (2017).
  • Skulnick, H. I., et al., Pyrimidinones. 2-Amino-5-halo-6-aryl-4(3H)-pyrimidinones. Interferon-inducing antiviral agents, Journal of Medicinal Chemistry, 28, 1864–1869, (1985).
  • Gangjee, A., Adair, O. ve Queener, S. F., Synthesis of 2,4-diamino-6-(thioarylmethyl)pyrido[2,3-d]pyrimidines as dihydrofolate reductase inhibitors. Bioorganic & Medicinal Chemistry, 9, 2929–2935, (2001).
  • Hunt, W. E., Schwalbe, C. H., Bird, K. ve Mallinson, P. D., Crystallographic and molecular-orbital studies on the geometry of antifolate drugs, Biochemical Journal, 187, 533–536, (1980).
  • Baker, B. R. ve Santi, D. V., Analogs of tetrahydrofolic acid XXIV: Further observations on the mode of pyrimidyl binding to dihydrofolic reductase and thymidylate synthetase by the 2-amino-5-(3-anilinopropyl)-6-methyl-4-pyrimidinol type of ınhibitor, Journal of Pharmaceutical Sciences, 54, 1252–1257, (1965).
  • Sharma, V., Chitranshi, N. ve Agarwal, A. K., Significance and biological importance of pyrimidine in the microbial World, International Journal of Medicinal Chemistry, 2014, 202784, (2014).
  • Singh, S. et al. Naturally ınspired pyrimidines analogues for Alzheimer’s Disease, Current Neuropharmacology, 19, 136–151, (2021).
  • Jubeen, F., et al., Eco-friendly synthesis of pyrimidines and its derivatives: A review on broad spectrum bioactive moiety with huge therapeutic profile, Synthetic Communications, 48, 601–625, (2018).
  • Howard, A., McIver, J. ve Collinst, J., HyperChem Computational Chemistry. Hypercube Inc., (1994).
  • Ayala, P. Y. ve Scuseria, G. E., Linear scaling second-order Moller–Plesset theory in the atomic orbital basis for large molecular systems, The Journal of Chemical Physics, 110, 3660–3671, (1999).
  • Muthu, S. ve Uma Maheswari, J., Quantum mechanical study and spectroscopic (FT-IR, FT-Raman, 13C, 1H, UV) study, first order hyperpolarizability, NBO analysis, HOMO and LUMO analysis of 4-[(4-aminobenzene) sulfonyl] aniline by ab initio HF and density functional method, Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 92, 154–163, (2012).
  • Kumer, A., Sarker, M. N. ve Paul, S., The theoretical investigation of HOMO, LUMO, thermophysical properties and QSAR study of some aromatic carboxylic acids using HyperChem programming, International Journal of Chemistry and Technology, 1, 26–37, (2019).
  • Kaya, A. ve Azizoglu, A., Abietan iskeletine sahip szemaoenoid a molekülünün teorik olarak incelenmesi, Süleyman Demirel Üniversitesi Fen Edebiyat Fakültesi Fen Dergisi, 17 (1), 82–95 (2022).
  • Koopmans, T., Über die Zuordnung von Wellenfunktionen und Eigenwerten zu den Einzelnen Elektronen Eines Atoms, Physica, 1, 104–113, (1934).
  • Çakır, F., Mikrodalga Yöntemiyle Karbazol Türevlerinin Sentezi, Karakterizasyonu ve Hesapsal Çalışmaları, Yüksek Lisans Tezi, Balıkesir Üniversitesi, Fen Bilimleri Enstitüsü, Balıkesir, (2020).

In silico investigation of the structural properties of some new N-substituted amino acid esters

Yıl 2023, Cilt: 25 Sayı: 2, 748 - 760, 07.07.2023

Ümit Çalışır Baki Çiçek

https://doi.org/10.25092/baunfbed.1310449

Öz

Within the scope of this study, the HyperChem software was used to compute several theoretical (computational) properties of N-substituted glycine ester molecules, which have significant biological applications. The bond lengths, total charge density and charge distribution, and electrostatic potentials were calculated for ethyl 9-{[(2-ethoxy-2-oxoethyl)amino]ethyl}-4-oxo-3-oxa-6,9,12-triazatetradecane-14-oate (1), diethyl 3,6,9,12,15-pentaazaheptadecane-1,17-dioate (2), and ethyl 2-((6-methyl-2-pyridinyl)amino)acetate (3) compounds. Over their most stable configurations, several energy parameters as well as HOMO, LUMO, and ΔE orbitals were estimated. The ionization potential was calculated using the data that was collected. In addition, theoretical electronic UV spectrum and transition values were calculated The computed transition values and theoretical UV spectra were compared to the UV-VIS spectrum measured empirically. The compatibility of the theoretical and experimental evidence has been shown. Compound (3) has a very low ΔE value (8.8559 eV), which is a measure of a compound's reactivity.

Anahtar Kelimeler

N-substituted amino acid esters in silico HyperChem theoretical (computational) chemistry.

Kaynakça

  • Çalışır, Ü. ve Çiçek, B., Synthesis, characterization and determination of some theoretical properties of ethyl 2-((4,6-dimethylpyrimidin-2- yl)amino)acetate, Proceedings, III. International Siirt Conference on Scientific, 686–696, ISPEC Publishing House, (2022).
  • Culf, A. S. ve Ouellette, R. J., Solid-phase synthesis of N-substituted glycine oligomers (alpha-peptoids) and derivatives, Molecules, 15, 5282–5335, (2010).
  • Seo, J., Lee, B.-C. ve Zuckermann, R. N., Peptoids: Synthesis, Characterization, and Nanostructures, Comprehensive Biomaterials, 53–76, Elsevier, (2011).
  • Wetzer, M., Kapoor, R., Huang, W. ve Barron, A. E., Peptoid Oligomers: Peptidomimetics for Diverse Biomedical Applications, Polymer Science: A Comprehensive Reference, 267–287, Elsevier, (2012).
  • Bolt, H. L., Kleijn, L. H. J., Martin, N. I. ve Cobb, S. L., Synthesis of antibacterial nisin–peptoid hybrids using click methodology, Molecules, 23, 1–9, (2018).
  • Zuckermann, R. N., et al., Discovery of nanomolar ligands for 7-transmembrane G-protein-coupled receptors from a diverse N-(substituted)glycine peptoid library, Journal of Medicinal Chemistry, 37, 2678–2685, (1994).
  • Pospíšil, Š., et al., Epigenetic pyrimidine nucleotides in competition with natural dNTPs as substrates for diverse DNA polymerases, ACS Chemical Biology, 17, 2781–2788, (2022).
  • House, D. A., Ammonia \ N-donor ligands, Encyclopedia of Inorganic Chemistry, John Wiley & Sons Ltd, (2006).
  • Sigma Aldrich, Tris(2-aminoethyl)amine, Sigma Aldrich Co., (2022).
  • Pawlaczyk, M. ve Schroeder, G., Adsorption studies of Cu(II) ions on dendrimer-grafted silica-based materials, Journal of Molecular Liquids, 281, 176–185, (2019).
  • Fan, Y., et al., Synthesis and aggregation behavior of a hexameric quaternary ammonium surfactant, Langmuir, 27, 10570–10579, (2011).
  • Patras, G., Qiao, G. G., Solomon, D. H. ve Koch, R., Synthesis, characterization, and modelling of novel multifunctional acryloyl-based monomers: an experimental and computational study, Australian Journal of Chemistry, 55, 675–680, (2002).
  • Afrin, R., Shah, N. A., Abbas, M., Amin, M. ve Bhatti, A. S., Sensors and actuators A : Physical design and analysis of functional multiwalled carbon nanotubes for infrared sensors, Sensors Actuators A, 203, 203, 142–148, (2013).
  • Vasil’eva, S. V., Abramova, T. V., Ivanova, T. M., Shishkin, G. V. ve Sil’nikov, V. N., Monomers for oligonucleotide synthesis with linkers carrying reactive residues: II. The synthesis of phosphoamidites on the basis of uridine and cytosine and containing a linker with methoxyoxalamide groups in position 2′, Russian Journal of Bioorganic Chemistry, 30, 234–242, (2004).
  • Zain-ul-Abdin et al, Tris(2-aminoethyl)amine-based ferrocene-terminated dendrimers as burning rate catalysts for ammonium perchlorate-based propellant decomposition, Applied Organometallic Chemistry, 32, 1–11, (2018).
  • Rawal, R. K., Dutta, B. ve Patel, P., Pyrimidine ring containing natural products and their biological importance, Pyrimidines And Their Importance, Nova Science Publishers, (2023).
  • Lagoja, I. M., Pyrimidine as constituent of natural biologically active compounds. Chemistry & Biodiversity, 2, 1–50, (2005).
  • Madhavan, G. R., et al., Synthesis and biological activity of novel pyrimidinone containing thiazolidinedione derivatives, Bioorganic & Medicinal Chemistry, 10, 2671–2680, (2002).
  • Gichinga, M. G., et al., Synthesis and evaluation of metabotropic glutamate receptor subtype 5 antagonists based on fenobam, ACS Medicinal Chemistry Letters, 2, 882–884, (2011).
  • Pretorius, S. I., Breytenbach, W. J., de Kock, C., Smith, P. J. ve N’Da, D. D., Synthesis, characterization and antimalarial activity of quinoline-pyrimidine hybrids, Bioorganic & Medicinal Chemistry, 21, 269–277, (2013).
  • Zuniga, E. S., et al., The synthesis and evaluation of triazolopyrimidines as anti-tubercular agents, Bioorganic & Medicinal Chemistry, 25, 3922–3946, (2017).
  • Skulnick, H. I., et al., Pyrimidinones. 2-Amino-5-halo-6-aryl-4(3H)-pyrimidinones. Interferon-inducing antiviral agents, Journal of Medicinal Chemistry, 28, 1864–1869, (1985).
  • Gangjee, A., Adair, O. ve Queener, S. F., Synthesis of 2,4-diamino-6-(thioarylmethyl)pyrido[2,3-d]pyrimidines as dihydrofolate reductase inhibitors. Bioorganic & Medicinal Chemistry, 9, 2929–2935, (2001).
  • Hunt, W. E., Schwalbe, C. H., Bird, K. ve Mallinson, P. D., Crystallographic and molecular-orbital studies on the geometry of antifolate drugs, Biochemical Journal, 187, 533–536, (1980).
  • Baker, B. R. ve Santi, D. V., Analogs of tetrahydrofolic acid XXIV: Further observations on the mode of pyrimidyl binding to dihydrofolic reductase and thymidylate synthetase by the 2-amino-5-(3-anilinopropyl)-6-methyl-4-pyrimidinol type of ınhibitor, Journal of Pharmaceutical Sciences, 54, 1252–1257, (1965).
  • Sharma, V., Chitranshi, N. ve Agarwal, A. K., Significance and biological importance of pyrimidine in the microbial World, International Journal of Medicinal Chemistry, 2014, 202784, (2014).
  • Singh, S. et al. Naturally ınspired pyrimidines analogues for Alzheimer’s Disease, Current Neuropharmacology, 19, 136–151, (2021).
  • Jubeen, F., et al., Eco-friendly synthesis of pyrimidines and its derivatives: A review on broad spectrum bioactive moiety with huge therapeutic profile, Synthetic Communications, 48, 601–625, (2018).
  • Howard, A., McIver, J. ve Collinst, J., HyperChem Computational Chemistry. Hypercube Inc., (1994).
  • Ayala, P. Y. ve Scuseria, G. E., Linear scaling second-order Moller–Plesset theory in the atomic orbital basis for large molecular systems, The Journal of Chemical Physics, 110, 3660–3671, (1999).
  • Muthu, S. ve Uma Maheswari, J., Quantum mechanical study and spectroscopic (FT-IR, FT-Raman, 13C, 1H, UV) study, first order hyperpolarizability, NBO analysis, HOMO and LUMO analysis of 4-[(4-aminobenzene) sulfonyl] aniline by ab initio HF and density functional method, Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 92, 154–163, (2012).
  • Kumer, A., Sarker, M. N. ve Paul, S., The theoretical investigation of HOMO, LUMO, thermophysical properties and QSAR study of some aromatic carboxylic acids using HyperChem programming, International Journal of Chemistry and Technology, 1, 26–37, (2019).
  • Kaya, A. ve Azizoglu, A., Abietan iskeletine sahip szemaoenoid a molekülünün teorik olarak incelenmesi, Süleyman Demirel Üniversitesi Fen Edebiyat Fakültesi Fen Dergisi, 17 (1), 82–95 (2022).
  • Koopmans, T., Über die Zuordnung von Wellenfunktionen und Eigenwerten zu den Einzelnen Elektronen Eines Atoms, Physica, 1, 104–113, (1934).
  • Çakır, F., Mikrodalga Yöntemiyle Karbazol Türevlerinin Sentezi, Karakterizasyonu ve Hesapsal Çalışmaları, Yüksek Lisans Tezi, Balıkesir Üniversitesi, Fen Bilimleri Enstitüsü, Balıkesir, (2020).
Toplam 35 adet kaynakça vardır.

Ayrıntılar

Birincil Dil Türkçe
Konular Fiziksel Organik Kimya, Hesaplamalı Kimya
Bölüm Araştırma Makalesi
Yazarlar

Ümit Çalışır 0000-0001-7699-2008

Baki Çiçek 0000-0003-1257-1188

Erken Görünüm Tarihi 6 Temmuz 2023
Yayımlanma Tarihi 7 Temmuz 2023
Gönderilme Tarihi 6 Haziran 2023
Yayımlandığı Sayı Yıl 2023 Cilt: 25 Sayı: 2

Kaynak Göster

APA Çalışır, Ü., & Çiçek, B. (2023). Bazı yeni N-sübstitüe amino asit esterlerinin yapısal özelliklerinin in silico ile araştırılması. Balıkesir Üniversitesi Fen Bilimleri Enstitüsü Dergisi, 25(2), 748-760. https://doi.org/10.25092/baunfbed.1310449
AMA Çalışır Ü, Çiçek B. Bazı yeni N-sübstitüe amino asit esterlerinin yapısal özelliklerinin in silico ile araştırılması. BAUN Fen. Bil. Enst. Dergisi. Temmuz 2023;25(2):748-760. doi:10.25092/baunfbed.1310449
Chicago Çalışır, Ümit, ve Baki Çiçek. “Bazı Yeni N-sübstitüe Amino Asit Esterlerinin yapısal özelliklerinin in Silico Ile araştırılması”. Balıkesir Üniversitesi Fen Bilimleri Enstitüsü Dergisi 25, sy. 2 (Temmuz 2023): 748-60. https://doi.org/10.25092/baunfbed.1310449.
EndNote Çalışır Ü, Çiçek B (01 Temmuz 2023) Bazı yeni N-sübstitüe amino asit esterlerinin yapısal özelliklerinin in silico ile araştırılması. Balıkesir Üniversitesi Fen Bilimleri Enstitüsü Dergisi 25 2 748–760.
IEEE Ü. Çalışır ve B. Çiçek, “Bazı yeni N-sübstitüe amino asit esterlerinin yapısal özelliklerinin in silico ile araştırılması”, BAUN Fen. Bil. Enst. Dergisi, c. 25, sy. 2, ss. 748–760, 2023, doi: 10.25092/baunfbed.1310449.
ISNAD Çalışır, Ümit - Çiçek, Baki. “Bazı Yeni N-sübstitüe Amino Asit Esterlerinin yapısal özelliklerinin in Silico Ile araştırılması”. Balıkesir Üniversitesi Fen Bilimleri Enstitüsü Dergisi 25/2 (Temmuz 2023), 748-760. https://doi.org/10.25092/baunfbed.1310449.
JAMA Çalışır Ü, Çiçek B. Bazı yeni N-sübstitüe amino asit esterlerinin yapısal özelliklerinin in silico ile araştırılması. BAUN Fen. Bil. Enst. Dergisi. 2023;25:748–760.
MLA Çalışır, Ümit ve Baki Çiçek. “Bazı Yeni N-sübstitüe Amino Asit Esterlerinin yapısal özelliklerinin in Silico Ile araştırılması”. Balıkesir Üniversitesi Fen Bilimleri Enstitüsü Dergisi, c. 25, sy. 2, 2023, ss. 748-60, doi:10.25092/baunfbed.1310449.
Vancouver Çalışır Ü, Çiçek B. Bazı yeni N-sübstitüe amino asit esterlerinin yapısal özelliklerinin in silico ile araştırılması. BAUN Fen. Bil. Enst. Dergisi. 2023;25(2):748-60.