Cyclo(Tyr-Tyr) Dipeptidinin Teorik IR, Raman ve Moleküler Yapı Analizi

Year 2021, Volume 25, Issue 2, 401 - 409, 20.08.2021

Sefa ÇELİK Sevim AKYÜZ Ayşen ÖZEL

https://doi.org/10.19113/sdufenbed.881399

Abstract

Bu çalışmada HT-29, Hela ve MCF-7 hücre hatlarına karşı antikanser etki gösteren Cyclo(Tyr-Tyr) dipeptidinin olası en kararlı yedi konformasyonu tirozin aminoasilerinin χ yan zincir dihedral açılarına bağlı olarak konformasyon analizi yapılarak belirlenmiştir. Konformasyon analizi sonrasında belirlenen konformasyonlara ait geometrik yapılar, yan zincire ait dihedral açıdaki değişimler ve konformerlerin toplam ve bağıl enerjileri ile bu konformasyonların toplam enerjilerine katkı sağlayan van der Waals, elektrostatik, torsiyon enerji katkıları ayrı ayrı hesaplanmıştır. Ek olarak bu dipeptidin dimerik formu, kuantum kimyasal ab-initio hesaplamalarla optimize edilerek halka yapıya ait w, φ, Ψ dihedral açıları monomer form ile karşılaştırmalı olarak verilmiştir ve dimerik formu oluşturan moleküller arası hidrojen bağları belirlenmiştir.

Keywords

Cyclo(Tyr-Tyr), Dipeptit, Diketopiperazin, Konformasyon Analizi, Moleküler Modelleme

Theoretical IR, Raman and Molecular Structure Analysis of Cyclo (Tyr-Tyr) Dipeptide

Abstract

In this study, the most stable seven conformations of the Cyclo (Tyr-Tyr) dipeptide, which shows anticancer effect against HT-29, Hela, and MCF-7 cell lines, were determined by conformational analysis based on χ side-chain dihedral angles of the two tyrosine amino acids. The geometric structures of the conformations, determined after the conformation analysis, the changes in the dihedral angle of the side-chain, the total and relative energies of the conformers, and the van der Waals, electrostatic and torsion energy contributions, that contribute to the total energies, were calculated separately. The most stable conformer, determined by conformation analysis, was then optimized using density functional theory (DFT), B3LYP functional and the 6-31++G(d,p) basis set by using Gaussian03 program, and the fundamental vibrational wavenumbers of the optimized structure were calculated at the same level of theory. In addition, IR intensities, Raman activities, potential energy distributions were determined using the MOLVIB program, and the scaled Raman activities scaled were transformed into Raman intensities by Simirra program. Furthermore, the dimeric form of the dipeptide was created and optimized at the DFT/B3LYP/6-31G(d,p) level of theory. The w, φ, Ψ dihedral angles of the ring structure were given comparatively with the monomer form calculated with the same basis sets. The intermolecular hydrogen bonds that play role in the formation of the dimeric structure have been determined.

Keywords

Cyclo(Tyr-Tyr), Dipeptide, Diketopiperazine, Conformational analysis, Molecular modeling

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