Biyomoleküllere yönelik moleküler damgalanmış polimerler için hesapsal yaklaşım
Küçük Resim Yok
Tarih
2019
Yazarlar
Dergi Başlığı
Dergi ISSN
Cilt Başlığı
Yayıncı
Ege Üniversitesi
Erişim Hakkı
info:eu-repo/semantics/openAccess
Özet
Moleküler olarak damgalanmış polimerlerin (MIP'ler) hazırlanması zaman alıcıdır. MIP'lerin hazırlanma protokolleri, monomer seçimi, kalıp molekülü için uygun porojen, çapraz bağlayıcı ve stokiyometri oranını içerir. Hesapsal yöntemleri kullanmak, zaman ve maliyeti kısaltabilir. Hedef molekül ve monomerler için başlangıç yapıları oluşturmak için, Spartan 16'da konformasyonel dağılım uygulanmıştır. Kompleksler üzerinde çalışılmıştır. İlk geometriler, moleküler mekanik yöntemle konformasyonel dağılımla elde edildikten sonra, bu geometriler yarı ampirik yöntemlerle hesaplandı. Bir sonraki aşamada, kompleksler arasından enerji olarak en kararlı ve bazı daha az kararlı yapılar seçildi. Bu kompleksler için ayrıca Yoğunluk Foksiyoneli Teorisi (DFT) yöntemi kullanılarak daha yüksek seviyelerde hesaplamalar gerçekleştirildi. DFT çalışmalarında, bu yapılar Gaussian 09'da ?B97XD fonksiyoneli ve 6-311++G(d,p) baz seti ile hesaplanmıştır. MIP sisteminde solvent etkisini gözlemlemek için, hesaplamalarda Polarizable Continuum Model (PCM) kullanılmıştır. Ayrıca çapraz bağlayıcı moleküllerin pre-polimerizasyon kompleksine etkileri incelendi. Hidrojen bağları, moleküler olarak basılmış polimerlerin oluşumu ve stabilitesi için önemlidir. Hidrojen bağı etkileşiminden zayıf etkileşimler de moleküler tanımada etkilidir. Bu çalışmada bu etkileşimler ve MIP üzerindeki etkileri incelendi
Although it is relatively simple to prepare molecularly imprinted polymers (MIPs), it may be time consuming. Preparation protocols of MIPs include selection of monomer(s), proper porogen and crosslinker for template molecule, and relative stoichiometry ratio. Using computational methods may decrease required time and cost. To generate input structures for the target molecule and the monomers, conformational distribution in Spartan 16 was used. The complexes were studied in several ratios. After initial geometries were obtained from conformational distribution by molecular mechanics method, these geometries were calculated by semiempirical methods. In the next stage, selected complexes were used including the most stable ones and some others for further investigation. These complexes are also calculated using higher levels of theory with Density Functional Theory (DFT) method. In DFT studies, these structures were calculated with ?B97XD functional in combination with 6-311++G(d,p) basis set as implemented in Gaussian 09. For observing solvent effect on MIP systems, Polarizable Continuum Model (PCM) was used in calculations. Moreover, the effects of cross-linking molecules on the pre-polymerization complex were investigated. Hydrogen bonds are important for the formation and stability of molecularly imprinted polymers. Dispersion effects are also effective in molecular recognition. In this study, these interactions and their effects on MIP were investigated.
Although it is relatively simple to prepare molecularly imprinted polymers (MIPs), it may be time consuming. Preparation protocols of MIPs include selection of monomer(s), proper porogen and crosslinker for template molecule, and relative stoichiometry ratio. Using computational methods may decrease required time and cost. To generate input structures for the target molecule and the monomers, conformational distribution in Spartan 16 was used. The complexes were studied in several ratios. After initial geometries were obtained from conformational distribution by molecular mechanics method, these geometries were calculated by semiempirical methods. In the next stage, selected complexes were used including the most stable ones and some others for further investigation. These complexes are also calculated using higher levels of theory with Density Functional Theory (DFT) method. In DFT studies, these structures were calculated with ?B97XD functional in combination with 6-311++G(d,p) basis set as implemented in Gaussian 09. For observing solvent effect on MIP systems, Polarizable Continuum Model (PCM) was used in calculations. Moreover, the effects of cross-linking molecules on the pre-polymerization complex were investigated. Hydrogen bonds are important for the formation and stability of molecularly imprinted polymers. Dispersion effects are also effective in molecular recognition. In this study, these interactions and their effects on MIP were investigated.
Açıklama
Anahtar Kelimeler
Bilim ve Teknoloji, Science and Technology, Biyokimya, Biochemistry, Biyoteknoloji, Biotechnology, Biyopolimerler, Biopolymers
