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Journals / Balıkesir Üniversitesi Fen Bilimleri Enstitüsü Dergisi / 2023 / Cilt: 25 Sayı: 2

Hirshfeld surface analysis, interaction energy calculations and in silico anti-SARS-CoV-2 potentials of metal (II) 3,4-dimethoxybenzoate with nicotinamide complexes

Metal (II) 3,4-dimetoksibenzoatın nikotinamid komplekslerinin Hirshfeld yüzey analizi, etkileşim enerjisi hesaplamaları ve in silico anti-SARS-CoV-2 potansiyelleri

Füreya Elif Öztürkkan(Kafkas Üniversitesi)0000-0001-6376-4161
Afşin Ahmet Kaya(ONDOKUZ MAYIS ÜNİVERSİTESİ)0000-0003-2082-6478
Elif Çelenk Kaya(ONDOKUZ MAYIS ÜNİVERSİTESİ)0000-0002-7811-7669
Pages
599–613
Publication Date
2023-07-07
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AI Summary & Key Takeaways

AI Insight
⚡ TL;DR(Too Long; Didn't Read)

According to the results of the interaction energy analysis calculated with the help of B3LYP/6-31G(d,p), B3LYP/6-31G(d), B3LYP/3-21G, HF/6-31G(d,p), HF/6-31G(d), HF/3-21G, DFT/6-31G(d,p), DFT/6-31G(d), DFT/3-21G, MP2/6-31G(d,p), MP2/6-31G(d), MP2/3-21G basis sets, the major amount of the total energy is contributed by electrostatic and polarization energies.

📌 3 Key Takeaways

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Objective & Hypothesis:In this study, types of the intermolecular interactions, the intermolecular interaction energies, void analysis of diaquabis(3,4-dimethoxybenzoate)bis(nicotinamide)zinc(II) dihydrate (Complex 1), diaquabis(3,4-dimethoxybenzoate)bis(nicotinamide)nickel(II) dihydrate (Complex 2), diaquabis(3,4-dimethoxybenzoate)bis(nicotinamide)cobalt(II) dihydrate (Complex 3), whose crystal structures were characterized before, were investigated with the help of the CrystalExplorer program (Version 21.5).
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Key Findings & Data:According to the results of the interaction energy analysis calculated with the help of B3LYP/6-31G(d,p), B3LYP/6-31G(d), B3LYP/3-21G, HF/6-31G(d,p), HF/6-31G(d), HF/3-21G, DFT/6-31G(d,p), DFT/6-31G(d), DFT/3-21G, MP2/6-31G(d,p), MP2/6-31G(d), MP2/3-21G basis sets, the major amount of the total energy is contributed by electrostatic and polarization energies.
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Conclusion & Impact:The results determined as a result of interaction energy analysis and molecular docking studies show that the hydrogen bonds formed by the hydrogen bond donor/acceptor groups in the structure of the complexes are an important factor in both the stability of the crystal package and inhibition of important enzymes of SARS CoV-2.
🔬Design:Araştırma Makalesi
📍Scope:Comprehensive Sample
⚙️Variables:4-Dimetoksibenzoik asit · geçiş metal kompleksleri · Hirshfeld yüzey analizi

Abstract

In this study, types of the intermolecular interactions, the intermolecular interaction energies, void analysis of diaquabis(3,4-dimethoxybenzoate)bis(nicotinamide)zinc(II) dihydrate (Complex 1), diaquabis(3,4-dimethoxybenzoate)bis(nicotinamide)nickel(II) dihydrate (Complex 2), diaquabis(3,4-dimethoxybenzoate)bis(nicotinamide)cobalt(II) dihydrate (Complex 3), whose crystal structures were characterized before, were investigated with the help of the CrystalExplorer program (Version 21.5). It has been determined that H…H, H…O/O…H, H…C/C…H, H…N/N…H, C…C, C…O/O…C, O…O, and C…N/N…C interactions are intermolecular interactions that contribute to the Hirshfeld surface of the complexes. According to the results of the interaction energy analysis calculated with the help of B3LYP/6-31G(d,p), B3LYP/6-31G(d), B3LYP/3-21G, HF/6-31G(d,p), HF/6-31G(d), HF/3-21G, DFT/6-31G(d,p), DFT/6-31G(d), DFT/3-21G, MP2/6-31G(d,p), MP2/6-31G(d), MP2/3-21G basis sets, the major amount of the total energy is contributed by electrostatic and polarization energies. The interactions between Complexes 1-3 and the main protease enzyme and the spike protein of Omicron variant of the SARS-CoV-2 were investigated by Molecular docking studies. It was determined that complexes 1-3 and the main protease enzyme and the spike protein of Omicron variant of the SARS-CoV-2 interact via attractive charges, hydrogen bonding, electrostatic contacts, and hydrophobic interactions. According to the obtained results, further in vivo/in vitro studies are recommended for complex 3. The results determined as a result of interaction energy analysis and molecular docking studies show that the hydrogen bonds formed by the hydrogen bond donor/acceptor groups in the structure of the complexes are an important factor in both the stability of the crystal package and inhibition of important enzymes of SARS CoV-2.

Özet

Bu çalışmada, kristal yapıları daha önce karakterize edilmiş olan metal (II) 3,4-dimetoksibenzoatın nikotinamid komplekslerinin moleküllerarası etkileşim türleri, moleküllerarası etkileşim enerjileri ve boşluk analizi CrystalExplorer programı (Versiyon 21.5) yardımıyla incelenmiştir. H…H, H…O/O…H, H…C/C…H, H…N/N…H, C…C, C…O/O…C, O…O ve C…N/N…C etkileşimleri, komplekslerin Hirshfeld yüzeyine katkıda bulunan moleküller arası etkileşimlerdir. Hesaplanan etkileşim enerjisi analizi sonuçlarına göre, toplam enerjiye en önemli katkıyı elektrostatik ve polarizasyon enerjileri sağlamaktadır. Çalışmada ayrıca, kompleks 1-3 ile SARS CoV-2'nin ana proteaz enzimi ve Omicron varyantının spike proteini arasındaki etkileşimler Moleküler docking çalışmaları ile incelenmiştir. Kompleks 1-3'ün, yükler arası çekim kuvvetleri, hidrojen bağı, elektrostatik ve hidrofobik etkileşimler yoluyla SARS-CoV-2'nin ana proteaz enzimi ve Omicron varyantının spike proteini ile etkileşime girdiği belirlenmiştir. Elde edilen sonuçlara göre özellikle kompleks 3 için ileri in vivo/in vitro çalışmalar önerilmektedir. Etkileşim enerjisi analizi ve moleküler docking çalışmaları sonucunda belirlenen sonuçlar komplekslerin yapısında bulunan hidrojen bağı donor akseptor gruplar vasıtasıyla oluşan hidrojen bağlarının gerek kristal paketin kararlılığına gerekse SARS CoV-2'nin önemli enzimlerini inhibe etmede önemli birer faktör olduğunu göstermektedir.

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Cite This Article

Öztürkkan, F. E., Kaya, A. A., Kaya, E. Ç. (2023). Hirshfeld surface analysis, interaction energy calculations and in silico anti-SARS-CoV-2 potentials of metal (II) 3,4-dimethoxybenzoate with nicotinamide complexes. Balıkesir Üniversitesi Fen Bilimleri Enstitüsü Dergisi, Cilt: 25 Sayı: 2, 599–613. https://doi.org/10.25092/baunfbed.1203266

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